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.
I'm running Lion (OS X 10.7.1). Could that be contributing to the
problem?
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/.
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