OK, will try to get that .CEL to you. I should add that I've reproduced this error with multiple .CEL files. The COTES file was downloaded from TCGA and analysed by a colleague with aroma.affy without any problems.
Output of df is below: > df <- getFile(csR, 1); > print(df); AffymetrixCelFile: Name: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042 Tags: Full name: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042 Pathname: rawData/Test,set,Data/GenomeWideSNP_6/ COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042.CEL File size: 65.85 MB (69053496 bytes) RAM: 0.01 MB File format: v4 (binary; XDA) Platform: Affymetrix Chip type: GenomeWideSNP_6,Full Timestamp: 2008-07-13 15:02:08 On Aug 31, 11:16 am, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi. > > On Tue, Aug 30, 2011 at 5:45 PM, DGoode <dgoode.stanf...@gmail.com> wrote: > > Hi Henrik, > > > I think I got the same output you did - but I've pasted it below for > > you to check if you'd like. > > > Running diff only turned up differences in spacing at the end of > > lines. > > Ok. > > > > > I'm running Lion (OS X 10.7.1). Could that be contributing to the > > problem? > > I don't think so. > > Could you make your > 'COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042.CEL' file > available to me so I can try to reproduce it myself? Please gzip it. > > BTW, if you do > > df <- getFile(csR, 1); > print(df); > > what do you get? It should show the above CEL file - if not use > another index for getFile(). > > /Henrik > > > > > > > > > > > Thanks, > > David > > > ########################################## > > >> 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" > > > ########################################## > > > On Aug 31, 4:49 am, Henrik Bengtsson <henrik.bengts...@aroma- > > project.org> wrote: > >> 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</ch > >> > >> ipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341 > >> > >> 479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></src > >> > >> File><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>9 > >> 6968290</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 > > ... > > read more » -- 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/