Hi, it turns out that this was fixed in aroma.light v1.30.1(*). Now, aroma.light (>= 1.30.1) is part of Bioc v2.12 which is for R (>= 3.0.0). You are using R 2.15.1. So, in order for you do fix this problem, you have to upgrade R. This is something you should either way, because during the last 2 years lots of things have improved, several bug have been fixed and so on (both in R, BioC and aroma). Current stable release is R 3.1.0 (April 2014). Also, the next release of aroma.affymetrix et al. will require at least R (>= 3.0.1).
(*) Details from news(package="aroma.light"): Version: 1.30.1 [2013-04-18]: o BUG FIX: backtransformPrincipalCurve() gave an error if the pricipal curve was fitted using data with missing values. Hope this helps Henrik On Fri, May 2, 2014 at 1:33 AM, Clara Tang <clara...@gmail.com> wrote: > Dear Henrik, > > Thanks for your prompt reply. When I type sessionInfo(), the output is as > follows, > >>sessionInfo() > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8 > [5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] aroma.affymetrix_2.12.0 aroma.light_1.24.0 aroma.cn_1.5.0 > [4] aroma.core_2.12.1 R.devices_2.8.2 R.filesets_2.4.0 > [7] R.utils_1.29.8 R.oo_1.18.0 affxparser_1.28.1 > [10] R.methodsS3_1.6.1 > > loaded via a namespace (and not attached): > [1] aroma.apd_0.5.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.30.0 > [5] matrixStats_0.8.14 PSCBS_0.40.4 R.cache_0.9.2 R.huge_0.8.0 > [9] R.rsp_0.15.0 tools_2.15.1 > > Is there any problem with the version of Aroma files? I just updated them > recently but the workspace was built a while ago. > > Regards, > Clara > > > On Sunday, April 27, 2014 5:35:47 PM UTC+8, Clara Tang wrote: >> >> Hi, >> >> I am trying to perform cross platform normalization for CytoScan and Omni >> using MSCN but the program stops after smoothing. I imported the Affymetrix >> raw intensity data and called the totalCn and Baf using CRMAv2 and CalMate. >> LogR ratio (log2 scale) and BAF were extracted using GenomeStudio for Omni >> and imported as 2^LRR*2 and BAF into .total.asb and .fracB.asb respectively. >> Plotting the CN indicated similar level of mean intensities for both >> platforms (CN~1) and thereby I proceeded to perform the mscn. Smoothing >> looks normal but after that, the program seemed to stop while >> backtransforming. >> >> May I know how I can overcome the error of smooth.spline(sKK, lambda, >> ...)?? What's wrong in my data? >> >> Thanks a lot!!!!!! >> >> --Clara >> >> P.S. Log file is pasted as below, >> >> ===================================================== >> dsNList <- process(mscn, verbose=log) >> 20140427 17:06:46|Multi-source normalize all samples... >> 20140427 17:06:46| Number of unique samples in all sets: 8 >> chr [1:8] "9C" "9C-2" "2C" "2C-2" "4C" ... >> 20140427 17:06:46| Processing each array... >> 20140427 17:06:46| Sample #1 ('9C') of 8... >> 20140427 17:06:46| Identifying source data files... >> 20140427 17:06:46| Getting list tuple of data files for one sample... >> 20140427 17:06:46| Sample name: 9C >> 20140427 17:06:47| Number of arrays: 2 >> 20140427 17:06:47| Getting list tuple of data files for one >> sample...done >> [[1]] >> AromaUnitTotalCnBinaryFile: >> Name: 9C >> Tags: total >> Full name: 9C,total >> Pathname: >> totalAndFracBData/Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2/CytoScanHD_Array/9C,total.asb >> File size: 10.77 MB (11288937 bytes) >> RAM: 0.01 MB >> Number of data rows: 2822125 >> File format: v1 >> Dimensions: 2822125x1 >> Column classes: double >> Number of bytes per column: 4 >> Footer: <createdOn>20140421 18:35:53 >> HKT</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><srcDataSet>Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY</srcDataSet><srcChipType>CytoScanHD_Array,monocell</srcChipType><srcFullName>9C,chipEffects</srcFullName><srcChecksum>7d70e31c6aa60b7d8664373333ad5452</srcChecksum></srcFile> >> Platform: Affymetrix >> Chip type: CytoScanHD_Array >> >> [[2]] >> AromaUnitTotalCnBinaryFile: >> Name: 9C >> Tags:9C,ratio,total >> Full name: 9C,9C,ratio,total >> Pathname: totalAndFracBData/Omni/HumanOmni2.5/9C,9C,ratio,total.asb >> File size: 9.08 MB (9519600 bytes) >> RAM: 0.01 MB >> Number of data rows: 2379855 >> File format: v1 >> Dimensions: 2379855x1 >> Column classes: double >> Number of bytes per column: 4 >> Footer: <createdOn>20140427 16:14:31 >> HKT</createdOn><platform>Illumina</platform><chipType>HumanOmni2.5</chipType> >> Platform: Illumina >> Chip type: HumanOmni2.5 >> >> 20140427 17:06:47| Identifying source data files...done >> 20140427 17:06:47| Check if all arrays are already normalized... >> 20140427 17:06:47| Is done: FALSE >> 20140427 17:06:47| Check if all arrays are already normalized...done >> 20140427 17:06:47| Fitting model... >> 20140427 17:06:47| Fitting one sample across multiple sources... >> 20140427 17:06:47| Number of arrays: 2 >> 20140427 17:06:47| Sample name: 9C >> List of 4 >> $ subsetToFit : int [1:28781] 1 2 3 4 5 6 7 8 9 10 ... >> $ fitUgp :Classes 'AromaUgpFile', >> 'AromaUnitChromosomeTabularBinaryFile', 'AromaUnitTabularBinaryFile', >> 'UnitAnnotationDataFile', 'AromaMicroarrayTabularBinaryFile', >> 'AromaPlatformInterface', 'AromaTabularBinaryFile', 'FileCacheKeyInterface', >> 'CacheKeyInterface', 'GenericTabularFile', 'ColumnNamesInterface', >> 'GenericDataFile', 'FullNameInterface', 'Object' atomic [1:1] NA >> .. ..- attr(*, ".env")=<environment: 0x3c8f518> >> $ align : chr "byChromosome" >> $ targetDimension: int 1 >> 20140427 17:06:47| Getting list tuple of data files for one sample... >> 20140427 17:06:47| Sample name: 9C >> 20140427 17:06:47| Number of arrays: 2 >> 20140427 17:06:47| Getting list tuple of data files for one >> sample...done >> List of 2 >> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile', >> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface', >> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface', >> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile', >> 'FullNameInterface', 'Object' atomic [1:1] NA >> .. ..- attr(*, ".env")=<environment: 0x67be7f0> >> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile', >> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface', >> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface', >> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile', >> 'FullNameInterface', 'Object' atomic [1:1] NA >> .. ..- attr(*, ".env")=<environment: 0x36d2f48> >> 20140427 17:06:47| Extracting data... >> 20140427 17:06:47| Subset of units used for fitting: >> int [1:28781] 1 2 3 4 5 6 7 8 9 10 ... >> num [1:28781, 1:2] 0.561 0.566 0.798 0.861 0.81 ... >> V1 V2 >> Min. :-0.7285 Min. :-1.9090 >> 1st Qu.: 0.9677 1st Qu.: 0.9403 >> Median : 0.9842 Median : 0.9838 >> Mean : 0.9805 Mean : 0.9898 >> 3rd Qu.: 0.9995 3rd Qu.: 1.0340 >> Max. : 1.3343 Max. : 1.9075 >> NA's :1865 NA's :1934 >> 20140427 17:06:48| Extracting data...done >> 20140427 17:06:48| Fitting across-source normalization function... >> 20140427 17:06:48| Estimator for principal curves: >> function (Y, ...) >> - attr(*, "smoother")=function (lambda, xj, ...) >> - attr(*, "df")= num 5 >> 20140427 17:07:52| Fitting time: >> user system elapsed >> 63.884 0.008 64.062 >> 20140427 17:07:52| Direction of fitted curve ('lambda') was flipped >> such that it increases with the signal. >> 20140427 17:07:52| Processing time: 64.1 seconds >> List of 7 >> $ s : num [1:28781, 1:2] 0.652 0.652 0.665 NA 0.836 >> ... >> $ tag : num [1:28781] 15371 15372 7262 NA 15373 ... >> $ lambda : num [1:28781] 1.99 1.99 1.93 NA 1.38 ... >> $ dist : num 31.6 >> $ converged : logi TRUE >> $ nbrOfIterations: int 6 >> $ call : language principal.curve(x = X, smoother = ..1, >> trace = trace) >> - attr(*, "class")= chr [1:2] "PrincipalCurve" "principal.curve" >> - attr(*, "processingTime")=Class 'proc_time' Named num [1:5] 63.8 >> 0.004 63.975 0 0 >> .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" >> "elapsed" "user.child" ... >> 20140427 17:07:52| Fitting across-source normalization function...done >> 20140427 17:07:52| Calculating shift for each chromosome... >> 20140427 17:07:52| align=byChromosome >> 20140427 17:07:52| Chromosomes: 1-25 >> 20140427 17:07:52| Grouping units by chromosome... >> List of 24 >> $ Chr01: int [1:2472] 1 2 3 4 5 6 7 8 9 10 ... >> $ Chr02: int [1:2434] 2473 2474 2475 2476 2477 2478 2479 2480 2481 >> 2482 ... >> $ Chr03: int [1:1995] 4907 4908 4909 4910 4911 4912 4913 4914 4915 >> 4916 ... >> $ Chr04: int [1:1917] 6902 6903 6904 6905 6906 6907 6908 6909 6910 >> 6911 ... >> $ Chr05: int [1:1810] 8819 8820 8821 8822 8823 8824 8825 8826 8827 >> 8828 ... >> $ Chr06: int [1:1709] 10629 10630 10631 10632 10633 10634 10635 >> 10636 10637 10638 ... >> $ Chr07: int [1:1589] 12338 12339 12340 12341 12342 12343 12344 >> 12345 12346 12347 ... >> $ Chr08: int [1:1463] 13927 13928 13929 13930 13931 13932 13933 >> 13934 13935 13936 ... >> $ Chr09: int [1:1405] 15390 15391 15392 15393 15394 15395 15396 >> 15397 15398 15399 ... >> $ Chr10: int [1:1355] 16795 16796 16797 16798 16799 16800 16801 >> 16802 16803 16804 ... >> $ Chr11: int [1:1350] 18150 18151 18152 18153 18154 18155 18156 >> 18157 18158 18159 ... >> $ Chr12: int [1:1335] 19500 19501 19502 19503 19504 19505 19506 >> 19507 19508 19509 ... >> $ Chr13: int [1:1142] 20835 20836 20837 20838 20839 20840 20841 >> 20842 20843 20844 ... >> $ Chr14: int [1:1064] 21977 21978 21979 21980 21981 21982 21983 >> 21984 21985 21986 ... >> $ Chr15: int [1:1004] 23041 23042 23043 23044 23045 23046 23047 >> 23048 23049 23050 ... >> $ Chr16: int [1:900] 24045 24046 24047 24048 24049 24050 24051 >> 24052 24053 24054 ... >> $ Chr17: int [1:817] 24945 24946 24947 24948 24949 24950 24951 >> 24952 24953 24954 ... >> $ Chr18: int [1:778] 25762 25763 25764 25765 25766 25767 25768 >> 25769 25770 25771 ... >> $ Chr19: int [1:639] 26540 26541 26542 26543 26544 26545 26546 >> 26547 26548 26549 ... >> $ Chr20: int [1:637] 27179 27180 27181 27182 27183 27184 27185 >> 27186 27187 27188 ... >> $ Chr21: int [1:470] 27816 27817 27818 27819 27820 27821 27822 >> 27823 27824 27825 ... >> $ Chr22: int [1:496] 28286 28287 28288 28289 28290 28291 28292 >> 28293 28294 28295 ... >> $ Chr23: int [1:1550] 28782 28783 28784 28785 28786 28787 28788 >> 28789 28790 28791 ... >> $ Chr24: int [1:578] 30332 30333 30334 30335 30336 30337 30338 >> 30339 30340 30341 ... >> 20140427 17:07:52| Grouping units by chromosome...done >> 20140427 17:07:52| Allocating matrix for smooth data... >> 20140427 17:07:52| RAM: 494760 bytes >> 20140427 17:07:52| Allocating matrix for smooth data...done >> 20140427 17:07:52| Loading and backtransforming *smoothed* data... >> 20140427 17:07:52| Source #1 ('9C,total') of 2... >> 20140427 17:07:52| Loading smoothed data... >> num [1:30910] 0.561 0.566 0.798 0.861 0.81 ... >> 20140427 17:07:52| Loading smoothed data...done >> 20140427 17:07:52| Backtransforming smoothed data... >> Error in smooth.spline(sKK, lambda, ...) : >> missing or infinite values in inputs are not allowed >> 20140427 17:07:52| Backtransforming smoothed data...done >> 20140427 17:07:52| Source #1 ('9C,total') of 2...done >> 20140427 17:07:52| Loading and backtransforming *smoothed* >> data...done >> 20140427 17:07:52| Calculating shift for each chromosome...done >> 20140427 17:07:52| Fitting one sample across multiple sources...done >> 20140427 17:07:52| Fitting model...done >> 20140427 17:07:52| Sample #1 ('9C') of 8...done >> 20140427 17:07:52| Processing each array...done >> 20140427 17:07:52|Multi-source normalize all samples...done >> > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.