Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
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: createdOn20080710 22:47:02 PDT/createdOnplatformAffymetrix/platformchipTypeGenomeWideSNP_6/chipTypesrcFilefilenameGenomeWideSNP_6.probe_tab/filenamefilesize341479928/filesizechecksum2037c033c09fd8f7c06bd042a77aef15/checksum/srcFilesrcFile2filenameGenomeWideSNP_6.CN_probe_tab/filenamefilesize96968290/filesize checksum3dc2d3178f5eafdbea9c8b6eca88a89c/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$byName(Normal,TCGA,controls,and,778,Data, cdf=cdf) print(csNorms) AffymetrixCelSet: Name: Normal Tags: TCGA,controls,and,778,Data Path: rawData/Normal,TCGA,controls,and,778,Data/GenomeWideSNP_6 Platform: Affymetrix Chip type: GenomeWideSNP_6,Full Number of arrays: 29 Names: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042, COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G07_293052, COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G09_293056, ..., TOUSE_p_TCGAaffxB9_10a_N_GenomeWideSNP_6_E05_397070 [29] Time period: 2008-07-12 15:05:45 -- 2009-04-01 23:50:47 Total file size: 1910.19MB RAM: 0.03MB accNorms - AllelicCrosstalkCalibration(csNorms, model=CRMAv2) print(accNorms) AllelicCrosstalkCalibration: Data set: Normal Input tags:
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Hi. On Tue, Aug 30, 2011 at 5:45 PM, DGoode dgoode.stanf...@gmail.com wrote: Hi Henrik, I think I got the same output you did - but I've pasted it below for you to check if you'd like. Running diff only turned up differences in spacing at the end of lines. Ok. I'm running Lion (OS X 10.7.1). Could that be contributing to the problem? I don't think so. Could you make your 'COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042.CEL' file available to me so I can try to reproduce it myself? Please gzip it. BTW, if you do df - getFile(csR, 1); print(df); what do you get? It should show the above CEL file - if not use another index for getFile(). /Henrik Thanks, David ## cdf - AffymetrixCdfFile$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: createdOn20080710 22:47:02 PDT/createdOnplatformAffymetrix/ platformchipTypeGenomeWideSNP_6/ chipTypesrcFilefilenameGenomeWideSNP_6.probe_tab/ filenamefilesize341479928/filesize checksum2037c033c09fd8f7c06bd042a77aef15/checksum/ srcFilesrcFile2 filenameGenomeWideSNP_6.CN_probe_tab/filenamefilesize96968290/ filesize checksum3dc2d3178f5eafdbea9c8b6eca88a89c/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: createdOn20080710 22:47:02 PDT/createdOnplatformAffymetrix/platformchipTypeGenomeWideSNP_6/ch ipTypesrcFilefilenameGenomeWideSNP_6.probe_tab/filenamefilesize341 479928/filesizechecksum2037c033c09fd8f7c06bd042a77aef15/checksum/src FilesrcFile2filenameGenomeWideSNP_6.CN_probe_tab/filenamefilesize9 6968290/filesize checksum3dc2d3178f5eafdbea9c8b6eca88a89c/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) ==