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/
