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 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 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. 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/