Hi Henrik. Thanks for your reply. The output of sessionInfo() is below, after the output of the call to process().
Cheers, David > csC <- process(acc, verbose=verbose) Calibrating data set for allelic cross talk... Compressing model parameter to a short format... Compressing model parameter to a short format...done Calibrating 4 arrays... Path: probeData/Test,set,Data,ACC,ra,-XY/GenomeWideSNP_6 Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of 4... Error: length(pos) == ncol(cells) is not TRUE Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of 4...done Calibrating 4 arrays...done Calibrating data set for allelic cross talk...done > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] aroma.affymetrix_2.1.6 affxparser_1.24.0 aroma.apd_0.2.0 [4] R.huge_0.3.0 aroma.core_2.1.4 aroma.light_1.20.0 [7] matrixStats_0.2.2 R.rsp_0.6.2 R.cache_0.4.3 [10] R.filesets_1.1.0 digest_0.5.0 R.utils_1.7.8 [13] R.oo_1.8.1 R.methodsS3_1.2.1 On Aug 28, 10:05 am, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi, > > could you please us know what your sessionInfo() reports after > library(aroma.affymetrix) is called, or even, better after you get the > error? That will be key to troubleshooting this. > > /Henrik > > > > > > > > On Wed, Aug 24, 2011 at 11:00 PM, DGoode <dgoode.stanf...@gmail.com> wrote: > > Hi, I'm a new user of aroma.affymetrix. I run into a problem > > immediately after the allele crosstalk calibration step. I get the > > cryptic error "Error: length(pos) == ncol(cells) is not TRUE", but I > > can't seem to access the 'pos' or 'cells' variables. > > > I successfully completed all of the steps for CRMA v2 with a smaller > > data set but now I always encounter this problem. > > > Could someone please tell me what I might be overlooking or doing > > wrong? I haven't had any luck searching the group. > > > Thanks! > > > David > > >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") > >> csNorms <- AffymetrixCelSet$byName("Normal,TCGA,controls,and,778,Data", > >> cdf=cdf) > > >> print(csNorms) > > AffymetrixCelSet: > > Name: Normal > > Tags: TCGA,controls,and,778,Data > > Path: rawData/Normal,TCGA,controls,and,778,Data/GenomeWideSNP_6 > > Platform: Affymetrix > > Chip type: GenomeWideSNP_6,Full > > Number of arrays: 29 > > Names: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042, > > COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G07_293052, > > COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G09_293056, ..., > > TOUSE_p_TCGAaffxB9_10a_N_GenomeWideSNP_6_E05_397070 [29] > > Time period: 2008-07-12 15:05:45 -- 2009-04-01 23:50:47 > > Total file size: 1910.19MB > > RAM: 0.03MB > > >> accNorms <- AllelicCrosstalkCalibration(csNorms, model="CRMAv2") > >> print(accNorms) > > AllelicCrosstalkCalibration: > > Data set: Normal > > Input tags: TCGA,controls,and,778,Data > > User tags: * > > Asterisk ('*') tags: ACC,ra,-XY > > Output tags: TCGA,controls,and,778,Data,ACC,ra,-XY > > Number of files: 29 (1910.19MB) > > Platform: Affymetrix > > Chip type: GenomeWideSNP_6,Full > > Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200, > > subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr > > "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 > > 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98) > > Output path: probeData/Normal,TCGA,controls,and,778,Data,ACC,ra,-XY/ > > GenomeWideSNP_6 > > Is done: FALSE > > RAM: 0.01MB > > >> csC.Norms <- process(accNorms, verbose=verbose) > > Calibrating data set for allelic cross talk... > > Compressing model parameter to a short format... > > Compressing model parameter to a short format...done > > Calibrating 29 arrays... > > Path: probeData/Normal,TCGA,controls,and,778,Data,ACC,ra,-XY/ > > GenomeWideSNP_6 > > Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of > > 29... > > Error: length(pos) == ncol(cells) is not TRUE > > Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of > > 29...done > > Calibrating 29 arrays...done > > Calibrating data set for allelic cross talk...done > > Execution halted > > > -- > > 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 websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://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. 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