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</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"
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 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/
