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 »
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