Hi, I did get rid of the error message when I ran :
> unf <- TextUnitNamesFile$byChipType(chipType) I got this done by loading the aroma.affymetrix package, in addition to aroma.core. But now I got another error message when I followed Henrik's code at http://aroma-project.org/node/88 I was trying to creating data files containing log2 CN ratios. Everything was fine until I ran > units <- indexOf(unf, unitNames) Error in indexOf.UnitNamesFile(unf, unitNames) : [2012-05-16 14:53:18] Exception: If specified, argument 'pattern' must be a single string. Did you mean to use argument 'names'? at #02. indexOf.UnitNamesFile(unf, unitNames) - indexOf.UnitNamesFile() is in environment 'aroma.core' at #01. indexOf(unf, unitNames) - indexOf() is in environment 'R.filesets' > The command ran successfully when I tried to get units for certain probes > units <- indexOf(unf, names=c("A_16_P15025341","A_16_P00013121") + ) > units [1] 1006 1019 > I tried > ?indexOf.UnitNamesFile() and here is what I got: indexOf(this, pattern=NULL, names=NULL, ...) Arguments pattern A pattern to be used for identifying unit names of interest. If NULL <http://127.0.0.1:16952/library/base/html/NULL.html>, no regular expression matching is done. names Names to be match exactly to the unit names. ... Not used. What did I do wrong? Thanks a lot for the help! Ying > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_2.5.0 affxparser_1.28.0 aroma.apd_0.2.2 R.huge_0.3.0 [5] aroma.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.0 R.rsp_0.7.5 [9] R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2 R.utils_1.12.1 [13] R.oo_1.9.3 R.methodsS3_1.2.2 loaded via a namespace (and not attached): [1] tools_2.15.0 > On Tue, May 15, 2012 at 12:38 PM, sean nj <njs...@gmail.com> wrote: > Hi guys, > > I was following the Vignette: Creating binary data files containing copy > number estimates and trying to work on agilent HG-CGH-244A chip. I > downloaded and unzipped the .gz of the > HG-CGH-244A,TCGA,HB20080512,unitNames.txt and > HG-CGH-244A,TCGA,HB20080512.ugp and put them in > H:\Aroma_Analysis\annotationData\chipTypes\HG-CGH-244A folder. Then I tried > to run the same code on the vignette and got the error right away (please > see end of this email). Did I do something wrong? > > I have one more question regarding "Creating data files containing log2 CN > ratios" with HG-CGH-244A chip. The data I have are level 2 files from TCGA. > There is one txt file for each sample (not the original .asb file) and its > format is like: > > > Hybridization REF MSK_00001_251469322729_S01_CGH-v4_91 > > Composite Element REF normalizedLog2Ratio > > A_14_P112718 0.135431541355747 > > A_16_P15000916 0.441719513563848 > > A_16_P15001074 0.227252175271962 > > A_16_P00000012 0.231158251618718 > > A_16_P00000014 -0.0623833233443793 > > ......................................................... > > .......................................................... > > My first question is, does this kind data file work? > > My second question is, do I need to create a folder rawCnData as mentioned > in the vignette (Pathname: > rawCnData/MyDataSet,tagA,tagB/HG-CGH-244A/SampleA,tagA,tagB,log2ratio,total.asb)? > I also have the rawData folder which holds affy snp6 and expression data. > > > > Thanks a lot for the help! > > > > Ying > > > library(aroma.core) > > chipType <- "HG-CGH-244A" > > unf <- TextUnitNamesFile$byChipType(chipType) > Error in method(static, ...) : > [2012-05-15 12:12:26] Exception: Failed to create TextUnitNamesFile > object. Could to locate an annotation data file for chip type 'HG-CGH-244A' > (without requiring any tags) and with filename extension 'names' (this may > not be the correct extension as it was guessed from the class name > 'TextUnitNamesFile'). > at #02. method(static, ...) > - method() is in environment 'aroma.core' > at #01. TextUnitNamesFile$byChipType(chipType) > - TextUnitNamesFile$byChipType() is local of the calling function > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-mingw32/x64 (64-bit) > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] aroma.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.0 > R.rsp_0.7.5 R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2 > R.utils_1.12.1 > [9] R.oo_1.9.3 R.methodsS3_1.2.2 > > > > > > -- > 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/