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.
>
>
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>
--
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/
