Hi Zehla, this is most likely yet another thing caused by the fact that their code overrides the methods of aroma.affymetrix. It is simply too painful trying to troubleshoot what is going wrong when also loading their orphaned code which overwrites part of aroma.affymetrix. I might be able to find another patch like last time, but however much I wish to help you get through with your project, I'm not too keen spending time trying to patch their code (I've been there too many times already), even less so when they are not responding to either your or me. Their silence strongly suggests that they've orphaned the method/code and trying to get such to work is not fun and it often result in having to rewrite everything from scratch.
I recommend that you first make sure you can run CRMAv2 and CBS in aroma.affymetrix *without* loading any of their code/scripts. That asserts that you are using the correct annotation data etc. So, make sure you can do: 1. CRMAv2, e.g. http://aroma-project.org/vignettes/CRMAv2 2. CBS, e.g. http://aroma-project.org/vignettes/NonPairedCBS If that is giving you the same error, then there is something wrong with aroma.affymetrix that needs to be fixed. Cheers, Henrik On Thu, Dec 29, 2011 at 9:55 PM, Zelha Nil <zelh...@gmail.com> wrote: > Hi Henrik, > > > In the method I am using there is a problem again, and I could not find any > solution. > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > attached base packages: > [1] stats graphics grDevices datasets utils methods base > other attached packages: > [1] Cairo_1.5-0 RColorBrewer_1.0-5 signal_0.7-1 > MASS_7.3-16 gada_0.8-5 aroma.affymetrix_2.3.0 > [7] affxparser_1.26.1 aroma.apd_0.2.0 R.huge_0.3.0 > aroma.core_2.3.2 aroma.light_1.22.0 matrixStats_0.4.0 > [13] R.rsp_0.7.0 R.cache_0.5.2 R.filesets_1.1.3 > digest_0.5.1 R.utils_1.9.6 R.oo_1.8.3 > [19] R.methodsS3_1.2.1 > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > Warning message: > In method(static, ...) : > Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, > /gs, C:\Program Files\Common Files/gs >> getSummaryTableFromFile(segModel,"All") > Reading regions from file... > Reading genes from file... > [1] "2011-12-29 22:17:09 EET" > Error in getSummaryTableFromFile.CopyNumberSegmentationModel(segModel, : > argument "chromosomes" is missing, with no default > > I could not understand why it cannot find chromosomes?? The author of the > article still has not respond to my mail. If you can help me, I would > appreciate it. > > Thanx. > > > 17 Aralık 2011 13:12 tarihinde Zelha Nil <zelh...@gmail.com> yazdı: > >> Hi Henrik, >> >> >> The "rm" trick helped me :) it worked and I got the xls file. However, I >> found out that only one tumor or test sample could be used at each time.I >> had to change my data structure accordingly. >> >> Thanks so much .. >> >> Zelha Nil >> >> >> 2011/12/16 Henrik Bengtsson <henrik.bengts...@aroma-project.org> >>> >>> Hi. >>> >>> On Fri, Dec 16, 2011 at 3:16 AM, Zelha Nil <zelh...@gmail.com> wrote: >>> > I have contacted the authors about the problems many times but they did >>> > not >>> > return me. Because of that, I tried to contact you. >>> >>> I'm sorry to here. I've found the name "Alex" in the source code >>> comments, which I guess is first author Alex Lisovich (who has also >>> been >>> posting to this list in the past). I've cc him to see if I can bump >>> up this issue. >>> >>> TECHNICAL: The approach that was taken in this "extension" was to >>> cut'n'paste, "tune" and overwrite existing GADA and aroma.affymetrix >>> code, which makes it much less agile for changes in underlying >>> packages. A bigger concern is that this approach is very likely to >>> work with R v2.14.0 and beyond, because since then it is much harder >>> to overwrite existing code (due to so called namespaces). Alex, if >>> you read this, I'm happy to guide to do make your code more >>> sustainable (by basically extending the classes of aroma.affymetrix in >>> an object-oriented fashion instead of adjusting their code). >>> >>> My guesstimate is that the error you observe started to appear with >>> aroma.affymetrix v2.2.0 (April 2011). Note that this is not a >>> bug/problem with aroma.affymetrix, only with the "extension". >>> Unfortunately, it is rather common that published methods are >>> implemented once and not maintained. There are lots of reasons for >>> this, and there is a risk that the method you are trying to use is >>> one. If this is not the case here, I would have expected to authors >>> to have updated their code, because they will also run into this >>> problem each time they use their method. >>> >>> The best way to get their scripts working is to use an R version >>> before R v2.14.0 and install aroma.affymetrix v2.1.0 or before. That >>> is not a fun task to do, and I don't recommend it to anyone. >>> >>> > >>> > I did what you said. I deleted the files and run the program. Actually, >>> > after doing CRMAv2 we had to change the settings into aromadefault by >>> > using >>> > ">settings<-aromaDefaultSettings();". Then ı have run ref generation >>> > and >>> > segmentation. However, during report generation there was an error. >>> > (Error >>> > in paste("'", chromosomeLabels, "'", sep = "", collapse = ", ") : >>> > object 'chromosomeLabels' not found) I made it red below. How can you >>> > explain this? >>> >>> See if the following rm() "trick" will make it work: >>> >>> setupAromaExtensions(); >>> rm(updateSamplesFile.ChromosomeExplorer); >>> >>> Then continue "as usual". >>> >>> If you still run into problems, you could at least try to write the >>> regions file manually, by: >>> >>> segModel <- aromaSegmentation(ces1,ref,settings,verbose); >>> writeRegions(segModel, verbose=verbose); >>> >>> Now to what you're trying to achieve; if your CN data look really poor >>> ("noisy", "jumpy", "lots of aberrations all of the place", ...), it is >>> often due to low quality samples or a bad assay run. In such cases, >>> it is unlikely that an statistical method can rescue the true >>> biological signal. One can do a little bit, but don't expect magic. >>> >>> Hope this helps you go forward. Good luck with your thesis. >>> >>> /Henrik >>> >>> > >>> > >>> > >>> >> res<-aromaReports(segModel,"TEST",settings,verbose) >>> > 20111216 13:09:34|Generating ChromosomeExplorer report... >>> > 20111216 13:09:34| Setting up ChromosomeExplorer report files... >>> > 20111216 13:09:34| Copying template files... >>> > 20111216 13:09:34| Source path: >>> > >>> > C:/Users/bidbid/Documents/R/win-library/2.14/aroma.core/reports/includes >>> > 20111216 13:09:34| Destination path: reports/includes >>> > 20111216 13:09:35| Copying template files...done >>> > 20111216 13:09:35| Setting up ChromosomeExplorer report files...done >>> > 20111216 13:09:35| Copying ChromosomeExplorer.html... >>> > 20111216 13:09:35| Source pathname: >>> > >>> > C:/Users/bidbid/Documents/R/win-library/2.14/aroma.core/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html >>> > 20111216 13:09:35| Destination pathname: >>> > >>> > reports/TEST/ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY,a0.2,paired/ChromosomeExplorer.html >>> > 20111216 13:09:35| Copying ChromosomeExplorer.html...done >>> > 20111216 13:09:35| Explorer output version: 3 >>> > 20111216 13:09:35| Compiling ChromosomeExplorer.onLoad.js.rsp... >>> > 20111216 13:09:35| Source: >>> > >>> > C:/Users/bidbid/Documents/R/win-library/2.14/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp >>> > 20111216 13:09:36| Output path: >>> > reports/TEST/ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY,a0.2,paired >>> > 20111216 13:09:36| Scanning directories for available chip types... >>> > 20111216 13:09:36| Detected chip types: Mapping250K_Sty >>> > 20111216 13:09:36| Scanning directories for available chip >>> > types...done >>> > 20111216 13:09:36| Scanning image files for available zooms... >>> > 20111216 13:09:36| Detected (or default) zooms: 1, 2, 4, 8 >>> > 20111216 13:09:36| Scanning image files for available zooms...done >>> > 20111216 13:09:36| Scanning directory for subdirectories... >>> > 20111216 13:09:36| Detected (or default) sets: gada >>> > 20111216 13:09:36| Scanning directory for subdirectories...done >>> > 20111216 13:09:36| Compiling RSP... >>> > member data.class dimension objectSize >>> > 1 chipTypes character 1 104 >>> > 2 chrLayers character 0 40 >>> > 3 sampleLabels character 10 216 >>> > 4 sampleLayers character 0 40 >>> > 5 samples character 10 224 >>> > 6 sets character 1 96 >>> > 7 zooms numeric 4 56 >>> > 20111216 13:09:45| Sample names: >>> > [1] "arrays1" "arrays1" "arrays1" "arrays1" "arrays1" "arrays1" >>> > "arrays1" "arrays1" "arrays1" "arrays1" >>> > 20111216 13:09:45| Full sample names: >>> > [1] "arrays1,1" "arrays1,1" "arrays1,1" "arrays1,1" "arrays1,1" >>> > "arrays1,1" "arrays1,1" "arrays1,1" "arrays1,1" "arrays1,1" >>> > >>> > Error in paste("'", chromosomeLabels, "'", sep = "", collapse = ", ") : >>> > object 'chromosomeLabels' not found >>> > 20111216 13:09:45| Compiling RSP...done >>> > 20111216 13:09:45| Compiling ChromosomeExplorer.onLoad.js.rsp...done >>> > 20111216 13:09:45|Generating ChromosomeExplorer report...done >>> > >>> > Thank you for helping me :) >>> > >>> > >>> > >>> > 2011/12/16 Henrik Bengtsson <henrik.bengts...@aroma-project.org> >>> >> >>> >> Hi. >>> >> >>> >> On Fri, Dec 16, 2011 at 12:17 AM, Zelha Nil <zelh...@gmail.com> wrote: >>> >> > I am using the add on given in the article >>> >> > >>> >> > >>> >> > "http://ukpmc.ac.uk/articles/PMC3041647//reload=0;jsessionid=95C7FAD1718FE51219C497691EFD7209";. >>> >> > Package is available via: >>> >> > http://lnx02.dbmi.pitt.edu/download/Aroma%20Extensions.zip >>> >> >>> >> I had a quick look at this extension; you'll most likely have to >>> >> contact the authors of that extension, because I suspect that's where >>> >> the errors occur. However, I'll give you some guidance below. >>> >> >>> >> > >>> >> > >>> >> > I have set the wd as aroma.affymetirx folder. Then, I have used the >>> >> > arguments >>> >> > >>> >> > >>> >> >> source("setupAromaExtensions.R") >>> >> > Warning message: >>> >> > In readLines(file) : >>> >> > incomplete final line found on 'setupAromaExtensions.R' >>> >> > >>> >> >> setupAromaExtensions(); >>> >> > Loading required package: R.filesets >>> >> > Loading required package: digest >>> >> > R.filesets v1.1.3 (2011-09-26) successfully loaded. See ?R.filesets >>> >> > for >>> >> > help. >>> >> > >>> >> > Attaching package: ‘R.filesets’ >>> >> > >>> >> > The following object(s) are masked from ‘package:base’: >>> >> > >>> >> > append, readLines, sapply >>> >> > >>> >> > Loading required package: aroma.core >>> >> > Loading required package: R.cache >>> >> > R.cache v0.5.2 (2011-10-05) successfully loaded. See ?R.cache for >>> >> > help. >>> >> > >>> >> > >>> >> > Attaching package: ‘R.cache’ >>> >> > >>> >> > The following object(s) are masked from ‘package:R.filesets’: >>> >> > >>> >> > getChecksum >>> >> > >>> >> > Loading required package: R.rsp >>> >> > R.rsp v0.7.0 (2011-11-23) successfully loaded. See ?R.rsp for help. >>> >> > Type browseRsp() to open the RSP main menu in your browser. >>> >> > >>> >> > Attaching package: ‘R.rsp’ >>> >> > >>> >> > The following object(s) are masked from ‘package:R.filesets’: >>> >> > >>> >> > getHeader >>> >> > >>> >> > The following object(s) are masked from ‘package:base’: >>> >> > >>> >> > flush, restart, stop, write >>> >> > >>> >> > Loading required package: matrixStats >>> >> > matrixStats v0.4.0 (2011-11-11) successfully loaded. See >>> >> > ?matrixStats >>> >> > for >>> >> > help. >>> >> > Loading required package: aroma.light >>> >> > aroma.light v1.22.0 (2011-10-10) successfully loaded. See >>> >> > ?aroma.light >>> >> > for >>> >> > help. >>> >> > aroma.core v2.3.2 (2011-11-14) successfully loaded. See ?aroma.core >>> >> > for >>> >> > help. >>> >> > >>> >> > Attaching package: ‘aroma.core’ >>> >> > >>> >> > The following object(s) are masked from ‘package:base’: >>> >> > >>> >> > .Machine, append, apply, colMeans, colSums, library, require, >>> >> > sapply >>> >> > >>> >> > Loading required package: aroma.apd >>> >> > Loading required package: R.huge >>> >> > R.huge v0.3.0 (2011-07-23) successfully loaded. See ?R.huge for >>> >> > help. >>> >> > >>> >> > Attaching package: ‘R.huge’ >>> >> > >>> >> > The following object(s) are masked from ‘package:aroma.core’: >>> >> > >>> >> > readHeader >>> >> > >>> >> > The following object(s) are masked from ‘package:R.filesets’: >>> >> > >>> >> > getExtension, getFileSize, getPathname >>> >> > >>> >> > The following object(s) are masked from ‘package:base’: >>> >> > >>> >> > as.vector, colnames, flush, isOpen, ncol, nrow, rowMeans, >>> >> > rownames, >>> >> > rowSums >>> >> > >>> >> > Loading required package: affxparser >>> >> > aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd >>> >> > for >>> >> > help. >>> >> > aroma.affymetrix v2.3.0 (2011-10-28) successfully loaded. See >>> >> > ?aroma.affymetrix for help. >>> >> > >>> >> > Attaching package: ‘aroma.affymetrix’ >>> >> > >>> >> > The following object(s) are masked from ‘package:affxparser’: >>> >> > >>> >> > readCdfDataFrame, writeCdf >>> >> > >>> >> > The following object(s) are masked from ‘package:R.rsp’: >>> >> > >>> >> > write >>> >> > >>> >> > The following object(s) are masked from ‘package:grDevices’: >>> >> > >>> >> > boxplot.stats >>> >> > >>> >> > The following object(s) are masked from ‘package:methods’: >>> >> > >>> >> > getPackageName >>> >> > >>> >> > The following object(s) are masked from ‘package:base’: >>> >> > >>> >> > append, apply, colMeans, colSums, library, require, sapply, >>> >> > write >>> >> > >>> >> > Loading required package: MASS >>> >> > >>> >> > Attaching package: ‘signal’ >>> >> > >>> >> > The following object(s) are masked from ‘package:stats’: >>> >> > >>> >> > filter, poly >>> >> > >>> >> > The following object(s) are masked from ‘package:R.utils’: >>> >> > >>> >> > resample, unwrap >>> >> > >>> >> > Setup is done >>> >> > There were 50 or more warnings (use warnings() to see the first 50) >>> >> > >>> >> >> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE); >>> >> >> options(digits=4) >>> >> >> settings<-aromaDefaultSettings(); >>> >> >> doCRMAv2("allData", chipType="Mapping250K_Sty", plm="RmaCnPlm") >>> >> > AromaUnitTotalCnBinarySet: >>> >> > Name: allData >>> >> > Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY >>> >> > Full name: allData,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY >>> >> > Number of files: 19 >>> >> > Names: arrays1, arrays1, arrays1, ..., arrays2 [19] >>> >> > Path (to the first file): >>> >> > >>> >> > >>> >> > totalAndFracBData/allData,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty >>> >> > Total file size: 17.29 MB >>> >> > RAM: 0.02MB >>> >> > >>> >> >> >>> >> >> >>> >> >> >>> >> >> cesN<-aromaPreprocessing(dataSet="allData",chipType="Mapping250K_Sty",verbose=verbose) >>> >> > AffymetrixCdfFile: >>> >> > Path: annotationData/chipTypes/Mapping250K_Sty >>> >> > Filename: Mapping250K_Sty.cdf >>> >> > Filesize: 175.83MB >>> >> > Chip type: Mapping250K_Sty >>> >> > RAM: 0.00MB >>> >> > File format: v4 (binary; XDA) >>> >> > Dimension: 2560x2560 >>> >> > Number of cells: 6553600 >>> >> > Number of units: 238378 >>> >> > Cells per unit: 27.49 >>> >> > Number of QC units: 6 >>> >> > UgpGenomeInformation: >>> >> > Name: Mapping250K_Sty >>> >> > Tags: na31,HB20101007 >>> >> > Full name: Mapping250K_Sty,na31,HB20101007 >>> >> > Pathname: >>> >> > >>> >> > >>> >> > annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty,na31,HB20101007.ugp >>> >> > File size: 1.14 MB (1192508 bytes) >>> >> > RAM: 0.00 MB >>> >> > Chip type: Mapping250K_Sty >>> >> > UflSnpInformation: >>> >> > Name: Mapping250K_Sty >>> >> > Tags: na31,HB20101007 >>> >> > Full name: Mapping250K_Sty,na31,HB20101007 >>> >> > Pathname: >>> >> > >>> >> > >>> >> > annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty,na31,HB20101007.ufl >>> >> > File size: 466.18 kB (477371 bytes) >>> >> > RAM: 0.00 MB >>> >> > Chip type: Mapping250K_Sty >>> >> > Number of enzymes: 1 >>> >> > AromaCellSequenceFile: >>> >> > Name: Mapping250K_Sty >>> >> > Tags: HB20080710 >>> >> > Full name: Mapping250K_Sty,HB20080710 >>> >> > Pathname: >>> >> > >>> >> > annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty,HB20080710.acs >>> >> > File size: 162.50 MB (170394014 bytes) >>> >> > RAM: 0.00 MB >>> >> > Number of data rows: 6553600 >>> >> > File format: v1 >>> >> > Dimensions: 6553600x26 >>> >> > Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, >>> >> > raw, >>> >> > raw, >>> >> > raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw >>> >> > Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, >>> >> > 1, 1, >>> >> > 1, >>> >> > 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 >>> >> > Footer: <createdOn>20080710 21:11:58 >>> >> > >>> >> > >>> >> > PDT</createdOn><platform>Affymetrix</platform><chipType>Mapping250K_Sty</chipType><srcFile><filename>Mapping250K_Sty_probe_tab</filename><filesize>192816862</filesize><checksum>3e359c89f80ecdf1185a3dee55e40d3e</checksum></srcFile> >>> >> > Chip type: Mapping250K_Sty >>> >> > Platform: Affymetrix >>> >> > AffymetrixCelSet: >>> >> > Name: allData >>> >> > Tags: >>> >> > Path: rawData/allData/Mapping250K_Sty >>> >> > Platform: Affymetrix >>> >> > Chip type: Mapping250K_Sty >>> >> > Number of arrays: 19 >>> >> > Names: arrays1, arrays1, arrays1, ..., arrays2 [19] >>> >> > Time period: 2010-11-23 16:25:04 -- 2011-08-03 16:54:09 >>> >> > Total file size: 1196.53MB >>> >> > RAM: 0.02MB >>> >> > 20111216 10:00:28|Calibrating data set for allelic cross talk... >>> >> > 20111216 10:00:29| Already calibrated >>> >> > 20111216 10:00:29|Calibrating data set for allelic cross talk...done >>> >> > 20111216 10:00:30|Normalization data set for probe-sequence >>> >> > effects... >>> >> > 20111216 10:00:31| Already normalized >>> >> > 20111216 10:00:31|Normalization data set for probe-sequence >>> >> > effects...done >>> >> > 20111216 10:00:31|Fitting model of class RmaCnPlm... >>> >> > RmaCnPlm: >>> >> > Data set: allData >>> >> > Chip type: Mapping250K_Sty >>> >> > Input tags: ACC,-XY,BPN,-XY >>> >> > Output tags: ACC,-XY,BPN,-XY,RMA,A+B >>> >> > Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr >>> >> > "affyPLM"; >>> >> > treatNAsAs: chr "weights"; mergeStrands: logi TRUE; combineAlleles: >>> >> > logi >>> >> > TRUE). >>> >> > Path: plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty >>> >> > RAM: 0.00MB >>> >> > 20111216 10:00:31| Identifying non-estimated units... >>> >> > 20111216 10:00:31| Getting chip-effect set from data set... >>> >> > 20111216 10:00:31| Retrieving monocell CDF... >>> >> > 20111216 10:00:31| Monocell chip type: Mapping250K_Sty,monocell >>> >> > 20111216 10:00:31| Locating monocell CDF... >>> >> > 20111216 10:00:31| Pathname: >>> >> > >>> >> > annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty,monocell.CDF >>> >> > 20111216 10:00:31| Locating monocell CDF...done >>> >> > 20111216 10:00:32| Retrieving monocell CDF...done >>> >> > 20111216 10:00:32| Retrieving chip-effects from data set... >>> >> > 20111216 10:00:32| Data set: allData >>> >> > 20111216 10:00:32| Retrieving chip-effect #1 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,1,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #1 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #2 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,10,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #2 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #3 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,2,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #3 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #4 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,3,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #4 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #5 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,4,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #5 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #6 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,5,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #6 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #7 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,6,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #7 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #8 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,7,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #8 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #9 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,8,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #9 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #10 of 19 (arrays1)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays1,9,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #10 of 19 >>> >> > (arrays1)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #11 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,1,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #11 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #12 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,10,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #12 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #13 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,2,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #13 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #14 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,3,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #14 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #15 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,5,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #15 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #16 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,6,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #16 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #17 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,7,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #17 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #18 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,8,chipEffects.CEL >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #18 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:32| Retrieving chip-effect #19 of 19 (arrays2)... >>> >> > 20111216 10:00:32| Setting up CnChipEffectFile... >>> >> > 20111216 10:00:32| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,9,chipEffects.CEL >>> >> > 20111216 10:00:33| Setting up CnChipEffectFile...done >>> >> > 20111216 10:00:33| Retrieving chip-effect #19 of 19 >>> >> > (arrays2)...done >>> >> > 20111216 10:00:33| Retrieving chip-effects from data set...done >>> >> > 20111216 10:00:33| Getting chip-effect set from data set...done >>> >> > 20111216 10:00:33| Updating CnChipEffectSet... >>> >> > 20111216 10:00:33| Scanning for and applying sample annotation >>> >> > files... >>> >> > 20111216 10:00:33| Loading all SampleAnnotationSet:s... >>> >> > 20111216 10:00:33| Identifying all directories containing SAF >>> >> > files... >>> >> > 20111216 10:00:33| All SAF files located: >>> >> > [1] >>> >> > "annotationData/samples/HapMap270.saf" >>> >> > [2] >>> >> > >>> >> > >>> >> > "C:/Users/bidbid/Documents/R/win-library/2.14/aroma.affymetrix/annotationData/samples/HapMap270.saf" >>> >> > 20111216 10:00:33| All directories with SAF files: >>> >> > [1] >>> >> > "annotationData/samples" >>> >> > >>> >> > >>> >> > "C:/Users/bidbid/Documents/R/win-library/2.14/aroma.affymetrix/annotationData/samples" >>> >> > 20111216 10:00:33| Identifying all directories containing SAF >>> >> > files...done >>> >> > 20111216 10:00:33| Loading SampleAnnotationSet:s... >>> >> > 20111216 10:00:33| Defining 1 files... >>> >> > 1, >>> >> > 20111216 10:00:33| Defining 1 files...done >>> >> > 20111216 10:00:33| Defining 1 files... >>> >> > 1, >>> >> > 20111216 10:00:33| Defining 1 files...done >>> >> > [[1]] >>> >> > SampleAnnotationSet: >>> >> > Name: samples >>> >> > Tags: >>> >> > Full name: samples >>> >> > Number of files: 1 >>> >> > Names: HapMap270 [1] >>> >> > Path (to the first file): annotationData/samples >>> >> > Total file size: 0.03 MB >>> >> > RAM: 0.00MB >>> >> > >>> >> > [[2]] >>> >> > SampleAnnotationSet: >>> >> > Name: samples >>> >> > Tags: >>> >> > Full name: samples >>> >> > Number of files: 1 >>> >> > Names: HapMap270 [1] >>> >> > Path (to the first file): annotationData/samples >>> >> > Total file size: 0.03 MB >>> >> > RAM: 0.00MB >>> >> > >>> >> > 20111216 10:00:33| Loading SampleAnnotationSet:s...done >>> >> > 20111216 10:00:33| Reversing order of SampleAnnotationSet:s... >>> >> > [[1]] >>> >> > SampleAnnotationSet: >>> >> > Name: samples >>> >> > Tags: >>> >> > Full name: samples >>> >> > Number of files: 1 >>> >> > Names: HapMap270 [1] >>> >> > Path (to the first file): annotationData/samples >>> >> > Total file size: 0.03 MB >>> >> > RAM: 0.00MB >>> >> > >>> >> > [[2]] >>> >> > SampleAnnotationSet: >>> >> > Name: samples >>> >> > Tags: >>> >> > Full name: samples >>> >> > Number of files: 1 >>> >> > Names: HapMap270 [1] >>> >> > Path (to the first file): annotationData/samples >>> >> > Total file size: 0.03 MB >>> >> > RAM: 0.00MB >>> >> > >>> >> > 20111216 10:00:33| Reversing order of >>> >> > SampleAnnotationSet:s...done >>> >> > 20111216 10:00:33| Merging SampleAnnotationSet:s... >>> >> > SampleAnnotationSet: >>> >> > Name: samples >>> >> > Tags: >>> >> > Full name: samples >>> >> > Number of files: 2 >>> >> > Names: HapMap270, HapMap270 [2] >>> >> > Path (to the first file): annotationData/samples >>> >> > Total file size: 0.06 MB >>> >> > RAM: 0.00MB >>> >> > 20111216 10:00:33| Merging SampleAnnotationSet:s...done >>> >> > 20111216 10:00:33| Dropping duplicated files in >>> >> > SampleAnnotationSet:s... >>> >> > 20111216 10:00:33| Dropping 1 files that are identical to other >>> >> > files: >>> >> > [1] >>> >> > >>> >> > >>> >> > "C:/Users/bidbid/Documents/R/win-library/2.14/aroma.affymetrix/annotationData/samples/HapMap270.saf" >>> >> > SampleAnnotationSet: >>> >> > Name: samples >>> >> > Tags: >>> >> > Full name: samples >>> >> > Number of files: 1 >>> >> > Names: HapMap270 [1] >>> >> > Path (to the first file): annotationData/samples >>> >> > Total file size: 0.03 MB >>> >> > RAM: 0.00MB >>> >> > 20111216 10:00:33| Dropping duplicated files in >>> >> > SampleAnnotationSet:s...done >>> >> > 20111216 10:00:33| Loading all SampleAnnotationSet:s...done >>> >> > SampleAnnotationSet: >>> >> > Name: samples >>> >> > Tags: >>> >> > Full name: samples >>> >> > Number of files: 1 >>> >> > Names: HapMap270 [1] >>> >> > Path (to the first file): annotationData/samples >>> >> > Total file size: 0.03 MB >>> >> > RAM: 0.00MB >>> >> > 20111216 10:00:33| Scanning for and applying sample annotation >>> >> > files...done >>> >> > 20111216 10:00:33| Updating CnChipEffectSet...done >>> >> > 20111216 10:00:33| Identifying non-fitted units in chip-effect >>> >> > file... >>> >> > 20111216 10:00:33| Pathname: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/arrays2,9,chipEffects.CEL >>> >> > 20111216 10:00:33| Found indices cached on file >>> >> > 20111216 10:00:33| Reading data for these 238378 cells... >>> >> > 20111216 10:00:33| Reading data for these 238378 cells...done >>> >> > 20111216 10:00:33| Looking for stdvs <= 0 indicating non-estimated >>> >> > units: >>> >> > int(0) >>> >> > 20111216 10:00:33| Identifying non-fitted units in chip-effect >>> >> > file...done >>> >> > 20111216 10:00:33| Identifying non-estimated units...done >>> >> > 20111216 10:00:33| Getting model fit for 0 units. >>> >> > 20111216 10:00:33|Fitting model of class RmaCnPlm...done >>> >> > 20111216 10:00:33|Normalizing set for PCR fragment-length effects... >>> >> > 20111216 10:00:35| Already normalized >>> >> > 20111216 10:00:35| Getting output data set... >>> >> > 20111216 10:00:35| Getting output data set...done >>> >> > 20111216 10:00:35|Normalizing set for PCR fragment-length >>> >> > effects...done >>> >> > >>> >> >> ces1<-extract(cesN,"arrays1") >>> >> >> ces2<-extract(cesN,"arrays2"); >>> >> >> print(ces1) >>> >> > CnChipEffectSet: >>> >> > Name: allData >>> >> > Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY >>> >> > Path: >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty >>> >> > Platform: Affymetrix >>> >> > Chip type: Mapping250K_Sty,monocell >>> >> > Number of arrays: 10 >>> >> > Names: arrays1, arrays1, arrays1, ..., arrays1 [10] >>> >> > Time period: 2011-12-13 23:56:22 -- 2011-12-13 23:56:25 >>> >> > Total file size: 86.98MB >>> >> > RAM: 0.02MB >>> >> > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, >>> >> > combineAlleles: >>> >> > logi TRUE) >>> >> > >>> >> >> print(ces2) >>> >> > CnChipEffectSet: >>> >> > Name: allData >>> >> > Tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY >>> >> > Path: >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty >>> >> > Platform: Affymetrix >>> >> > Chip type: Mapping250K_Sty,monocell >>> >> > Number of arrays: 9 >>> >> > Names: arrays2, arrays2, arrays2, ..., arrays2 [9] >>> >> > Time period: 2011-12-13 23:56:26 -- 2011-12-13 23:56:29 >>> >> > Total file size: 78.29MB >>> >> > RAM: 0.02MB >>> >> > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, >>> >> > combineAlleles: >>> >> > logi TRUE) >>> >> > >>> >> >> ref<-aromaGetReference(ces1,ces2,settings,verbose) >>> >> > Getting VN reference set... >>> >> > Error in list(`aromaGetReference(ces1, ces2, settings, verbose)` = >>> >> > <environment>, : >>> >> > >>> >> > [2011-12-16 10:04:22] Exception: File already exists: >>> >> > >>> >> > >>> >> > plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty/.VN_REF_FILE.CEL >>> >> > at throw(Exception(...)) >>> >> > at throw.default("File already exists: ", pathname) >>> >> > at throw("File already exists: ", pathname) >>> >> > at method(static, ...) >>> >> > at Arguments$getWritablePathname(filename, path = path, mustExist >>> >> > = >>> >> > isFile, mustNotExist = !isFile) >>> >> > at pushTemporaryFile.default(pathname, verbose = verbose) >>> >> > at pushTemporaryFile(pathname, verbose = verbose) >>> >> > at BackShiftReference.R#439: createFrom.AffymetrixCelFile(ceRef1, >>> >> > filename >>> >> > = filename, path = getPath(ceRef1), methods = "create", clear = >>> >> > TRUE, >>> >> > verbose) >>> >> > at BackShiftReference.R#439: createFrom(ceRef1, filename = >>> >> > filename, >>> >> > path >>> >> > = getPath(ceRef1), methods = "create", clear = TRUE, verbose) >>> >> > at Processing.R#171: getBackShiftReferenceFile_Filter(testSet, >>> >> > refSet, >>> >> > name = VNSettings$VNRefFile, filter = filt, filterWidth = >>> >> > VNSettings$Filtering$filterWidth, chromosomes = VNSetting >>> >> > at >>> >> >>> >> The authors of the extension assumes that you only run that command >>> >> once, because it assumes that that the file: >>> >> >>> >> >>> >> >>> >> plmData/allData,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty/.VN_REF_FILE.CEL >>> >> >>> >> should not be there. My guess is that you can delete the file and >>> >> retry. >>> >> >>> >> >> aromaSettings$useGCCorrection<-TRUE; >>> >> >> aromaSettings$SegSettings$segType<-"GADA"; >>> >> >> segModel<-aromaSegmentation(ces1,ref=ces2,aromaSettings,verbose); >>> >> >>> >> So, are you using ref=ces2 because the above doesn't work, because in >>> >> the README.txt file they use ref=ref? If the latter, retry by first >>> >> deleting the above file. If you then get that original error, make >>> >> sure to report the verbose output you get. >>> >> >>> >> /Henrik >>> >> >>> >> > Performing segmentation...Error in list(`aromaSegmentation(ces1, ref >>> >> > = >>> >> > ces2, >>> >> > aromaSettings, verbose)` = <environment>, : >>> >> > >>> >> > [2011-12-16 10:06:46] Exception: The number of reference files does >>> >> > not >>> >> > match the number of sample files: 9 != 10 >>> >> > at throw(Exception(...)) >>> >> > at CopyNumberChromosomalModel.R#129: throw.default("The number of >>> >> > reference files does not match the number of sample files: ", >>> >> > nbrOfArrays(ref), " != ", nbrOfArrays(ces)) >>> >> > at CopyNumberChromosomalModel.R#129: throw("The number of >>> >> > reference >>> >> > files >>> >> > does not match the number of sample files: ", nbrOfArrays(ref), " != >>> >> > ", >>> >> > nbrOfArrays(ces)) >>> >> > at CopyNumberSegmentationModel.R#26: >>> >> > CopyNumberChromosomalModel(...) >>> >> > at CopyNumberSegmentationModel.R#26: >>> >> > extend(CopyNumberChromosomalModel(...), >>> >> > "CopyNumberSegmentationModel") >>> >> > at GadaModel.R#20: CopyNumberSegmentationModel(cesTuple = >>> >> > cesTuple, >>> >> > ...) >>> >> > at GadaModel.R#20: extend(CopyNumberSegmentationModel(cesTuple = >>> >> > cesTuple, >>> >> > ...), "GadaModel", GadaArgs = GadaArgs) >>> >> > at Processing.R#227: GadaModel(ces, ref, aAlpha = >>> >> > settings$SegSettings$GADA$aAlpha, T = settings$SegSettings$GADA$T, >>> >> > MinSegLen >>> >> > = sett >>> >> > >>> >> > >>> >> > These errors prevent me from report generation. However, once I can >>> >> > get >>> >> > all >>> >> > the VNref generation and segmentation successfully. However, after >>> >> > that >>> >> > time >>> >> > I can never do that again. Whatever, on that time, I could not >>> >> > generate >>> >> > any >>> >> > .xls reports. So I cannot go any further anlaysis (graphs dendogram >>> >> > heatmaps >>> >> > etc). Is there a problem in this add-on. >>> >> > >>> >> > Please help me. I should write my results as soon as possible >>> >> > because I >>> >> > will >>> >> > defend my thesis very soon. The reason why I am using this add-on is >>> >> > my >>> >> > data >>> >> > which is obtained from FFPE DNA samples and so very very noisy. I >>> >> > did >>> >> > tumorboost however, I could not get any normalization graph >>> >> > (tumor/normal) >>> >> > and results. >>> >> > >>> >> > Thank you .. >>> >> > >>> >> > >>> >> > >>> >> > 2011/12/15 Henrik Bengtsson <henrik.bengts...@aroma-project.org> >>> >> >> >>> >> >> Hi, >>> >> >> >>> >> >> what is your sessionInfo() and what does your R script look like? >>> >> >> >>> >> >> /Henrik >>> >> >> >>> >> >> On Thu, Dec 15, 2011 at 4:32 AM, Zelha Nil <zelh...@gmail.com> >>> >> >> wrote: >>> >> >> > Hi Henrik, >>> >> >> > >>> >> >> > There is a problem in creating regions.xls file, does not form >>> >> >> > at >>> >> >> > the >>> >> >> > end >>> >> >> > of the segmentation. Therefore, I could not get any plots, >>> >> >> > heatmaps, >>> >> >> > dendograms.. >>> >> >> > >>> >> >> > During report generation this error comes up: >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > Error in paste("'", chromosomeLabels, "'", sep = "", collapse = >>> >> >> > ", ") >>> >> >> > : >>> >> >> > object 'chromosomeLabels' not found >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > I searched the net for chromosome explorer and this object but I >>> >> >> > could >>> >> >> > not >>> >> >> > get any solutions. >>> >> >> > >>> >> >> > I am working on it, if you can clarify me about this error, I >>> >> >> > would >>> >> >> > appreciate it. >>> >> >> > >>> >> >> > Thank you. >>> >> >> > >>> >> >> > Best regards... >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > Zelha Nil >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > -- >>> >> >> > Zelha Nil >>> >> >> > >>> >> >> > "free me from freedom .." >>> >> >> > >>> >> >> > -- >>> >> >> > When reporting problems on aroma.affymetrix, make sure 1) to run >>> >> >> > the >>> >> >> > latest >>> >> >> > version of the package, 2) to report the output of sessionInfo() >>> >> >> > and >>> >> >> > traceback(), and 3) to post a complete code example. >>> >> >> > >>> >> >> > >>> >> >> > You received this message because you are subscribed to the >>> >> >> > Google >>> >> >> > Groups >>> >> >> > "aroma.affymetrix" group with website >>> >> >> > http://www.aroma-project.org/. >>> >> >> > To post to this group, send email to >>> >> >> > aroma-affymetrix@googlegroups.com >>> >> >> > To unsubscribe and other options, go to >>> >> >> > http://www.aroma-project.org/forum/ >>> >> >> >>> >> >> -- >>> >> >> When reporting problems on aroma.affymetrix, make sure 1) to run >>> >> >> the >>> >> >> latest version of the package, 2) to report the output of >>> >> >> sessionInfo() >>> >> >> and >>> >> >> traceback(), and 3) to post a complete code example. >>> >> >> >>> >> >> >>> >> >> You received this message because you are subscribed to the Google >>> >> >> Groups >>> >> >> "aroma.affymetrix" group with website >>> >> >> http://www.aroma-project.org/. >>> >> >> To post to this group, send email to >>> >> >> aroma-affymetrix@googlegroups.com >>> >> >> To unsubscribe and other options, go to >>> >> >> http://www.aroma-project.org/forum/ >>> >> > >>> >> > >>> >> > >>> >> > >>> >> > -- >>> >> > Zelha Nil >>> >> > >>> >> > "free me from freedom .." >>> >> > >>> >> > -- >>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the >>> >> > latest >>> >> > version of the package, 2) to report the output of sessionInfo() and >>> >> > traceback(), and 3) to post a complete code example. >>> >> > >>> >> > >>> >> > You received this message because you are subscribed to the Google >>> >> > Groups >>> >> > "aroma.affymetrix" group with website http://www.aroma-project.org/. >>> >> > To post to this group, send email to >>> >> > aroma-affymetrix@googlegroups.com >>> >> > To unsubscribe and other options, go to >>> >> > http://www.aroma-project.org/forum/ >>> >> >>> >> -- >>> >> When reporting problems on aroma.affymetrix, make sure 1) to run the >>> >> latest version of the package, 2) to report the output of >>> >> sessionInfo() and >>> >> traceback(), and 3) to post a complete code example. >>> >> >>> >> >>> >> You received this message because you are subscribed to the Google >>> >> Groups >>> >> "aroma.affymetrix" group with website http://www.aroma-project.org/. >>> >> To post to this group, send email to aroma-affymetrix@googlegroups.com >>> >> To unsubscribe and other options, go to >>> >> http://www.aroma-project.org/forum/ >>> > >>> > >>> > >>> > >>> > -- >>> > Zelha Nil >>> > >>> > "free me from freedom .." >>> > >>> > -- >>> > When reporting problems on aroma.affymetrix, make sure 1) to run the >>> > latest >>> > version of the package, 2) to report the output of sessionInfo() and >>> > traceback(), and 3) to post a complete code example. >>> > >>> > >>> > You received this message because you are subscribed to the Google >>> > Groups >>> > "aroma.affymetrix" group with website http://www.aroma-project.org/. >>> > To post to this group, send email to aroma-affymetrix@googlegroups.com >>> > To unsubscribe and other options, go to >>> > http://www.aroma-project.org/forum/ >>> >>> -- >>> When reporting problems on aroma.affymetrix, make sure 1) to run the >>> latest version of the package, 2) to report the output of sessionInfo() and >>> traceback(), and 3) to post a complete code example. >>> >>> >>> You received this message because you are subscribed to the Google Groups >>> "aroma.affymetrix" group with website http://www.aroma-project.org/. >>> To post to this group, send email to aroma-affymetrix@googlegroups.com >>> To unsubscribe and other options, go to >>> http://www.aroma-project.org/forum/ >> >> >> >> >> -- >> Zelha Nil >> >> "free me from freedom .." >> > > > > -- > Zelha Nil > > "free me from freedom .." > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
