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
--
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