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.



> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> csNorms <- AffymetrixCelSet$byName("Normal,TCGA,controls,and,778,Data", 
> cdf=cdf)
> print(csNorms)
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_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)
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/
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/
  Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of
Error: length(pos) == ncol(cells) is not TRUE
  Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of
 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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