Thanks, I already resolved the issue by replacing the CDF.
On Thursday, July 12, 2012 3:36:47 AM UTC+2, Henrik Bengtsson wrote:
>
> Before anything else, can you verify that your CDF is correct?
> Confirm that you get the following:
>
> > library("aroma.affymetrix");
> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> > cdf
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.CDF
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
> > getChecksum(cdf);
> [1] "3fbe0f6e7c8a346105238a3f3d10d4ec"
>
> /Henrik
>
> On Fri, Jul 6, 2012 at 7:07 AM, complexkid <tejalonl...@gmail.com> wrote:
> > Hi, I get the following error while running doASCRMAv2.
> > I may have found the problem, but I do not have solution (see below).
> Any
> > suggestions ??
> >
> > Thanks,
> > Tejal
> >
> >
> >>cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> >
> >>csR <- AffymetrixCelSet$byName("tcga_brca", cdf=cdf)
> >
> >>idxs <- indexOf(csR)
> >>setOption(aromaSettings, "memory/ram", 100.0)
> >>array=3
> >>csRx=extract(csR, idxs[array])
> >>doASCRMAv2(csRx, ram=200)
> >
> >
> > Error in `rownames<-`(`*tmp*`, value = c("A", "B")) :
> > length of 'dimnames' [1] not equal to array extent
> > In addition: Warning messages:
> > 1: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 2: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 3: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 4: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 5: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 6: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 7: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 8: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 9: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> > 10: In res[ii] <- resChunk :
> > number of items to replace is not a multiple of replacement length
> >
> > #### traceback
> >> traceback()
> > 12: `rownames<-`(`*tmp*`, value = c("A", "B"))
> > 11: cdfMergeAlleles(groups)
> > 10: getAlleleCellPairs.AffymetrixCdfFile(cdf, verbose = verbose)
> > 9: getAlleleCellPairs(cdf, verbose = verbose)
> > 8: getSetsOfProbes.AllelicCrosstalkCalibration(this, verbose =
> less(verbose,
> > 1))
> > 7: getSetsOfProbes(this, verbose = less(verbose, 1))
> > 6: process.AllelicCrosstalkCalibration(acc, verbose = verbose)
> > 5: process(acc, verbose = verbose)
> > 4: doCRMAv2.AffymetrixCelSet(..., combineAlleles = FALSE)
> > 3: doCRMAv2(..., combineAlleles = FALSE)
> > 2: doASCRMAv2.default(csRx, ram = 200)
> > 1: doASCRMAv2(csRx, ram = 200)
> >
> >
> > ############The error goes back to getCellIndices for the last "unit"
> > (uu=5570 in getAlleleCellPairs function).
> >
> >
> >> cells <- getCellIndices(cdf, units=units, stratifyBy="pm",
> useNames=F)
> >> uu <- 5570
> >> cells[[uu]]
> > $groups
> > $groups$A
> > $groups$A$indices
> > [1] 6814976 3029354
> >
> >
> > $groups$` ??`
> > $groups$` ??`$indices
> > integer(0)
> >
> >
> >
> > #### Here is the sessionInfo.
> >
> >> sessionInfo()
> > R version 2.15.0 (2012-03-30)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> > [1] C
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > other attached packages:
> > [1] multicore_0.1-7 aroma.cn_1.0.0
> aroma.affymetrix_2.5.0
> > [4] affxparser_1.28.0 aroma.apd_0.2.2 R.huge_0.3.0
> > [7] aroma.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.2
> > [10] R.rsp_0.8.2 R.devices_2.1.1 R.cache_0.6.2
> > [13] R.filesets_1.1.5 digest_0.5.2 R.utils_1.12.1
> > [16] R.oo_1.9.8 R.methodsS3_1.4.2
> >
> >
> > --
> > 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/.
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