Ok, your sessionInfo() looks good. Let's confirm that your annotation data files are correct. Do you get the same as I below - if not, let me know what you get:
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") > cdf AffymetrixCdfFile: Path: annotationData/chipTypes/GenomeWideSNP_6 Filename: GenomeWideSNP_6,Full.CDF Filesize: 470.44MB Chip type: GenomeWideSNP_6,Full RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 1881415 Cells per unit: 3.66 Number of QC units: 4 > getChecksum(cdf) [1] "3fbe0f6e7c8a346105238a3f3d10d4ec" > acs <- getAromaCellSequenceFile(cdf); > acs AromaCellSequenceFile: Name: GenomeWideSNP_6 Tags: HB20080710 Full name: GenomeWideSNP_6,HB20080710 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs File size: 170.92 MB (179217531 bytes) RAM: 0.00 MB Number of data rows: 6892960 File format: v1 Dimensions: 6892960x26 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 22:47:02 PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize> <checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2> Chip type: GenomeWideSNP_6 Platform: Affymetrix > getChecksum(acs) [1] "f04f081e0a1900653d957a8f320744c0" FYI, it is one of the internal sanity checks that catches the error. We've never experienced this ourselves and we've processed thousands of GenomeWideSNP_6 arrays. There is probably a simple answer to this. /Henrik On Tue, Aug 30, 2011 at 12:14 AM, DGoode <dgoode.stanf...@gmail.com> wrote: > 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. > > > 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. 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