hello,
I'am using the vignette Estimation of total copy numbers using the
CRMA v2 method (10K-GWS6) and I have problem when I want to execute
process.
The error is :
> acc2 <- AllelicCrosstalkCalibration(csR, model="CRMAv2",rescaleBy="all")
> acc2
AllelicCrosstalkCalibration:
Data set: Blood
Input tags:
User tags: *
Asterisk ('*') tags: ACC,-XY
Output tags: ACC,-XY
Number of files: 2 (125.28MB)
Platform: Affymetrix
Chip type: Mapping250K_Nsp
Algorithm parameters: (rescaleBy: chr "groups", targetAvg: num [1:2]
2200 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/Blood,ACC,-XY/Mapping250K_Nsp
Is done: FALSE
RAM: 0.01MB
> csC=process(acc2,verbose=verbose)
20110303 15:21:22|Calibrating data set for allelic cross talk...
Erreur dans if (any(units < 1)) stop("Argument 'units' contains non-
positive indices.") :
valeur manquante là où TRUE / FALSE est requis
20110303 15:21:22|Calibrating data set for allelic cross talk...done
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/C/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_2.0.0 aroma.apd_0.1.8
affxparser_1.22.1
[4] R.huge_0.2.2 aroma.core_2.0.0
aroma.light_1.18.3
[7] matrixStats_0.2.2 R.rsp_0.4.2
R.cache_0.4.0
[10] R.filesets_0.9.2 digest_0.4.2
R.utils_1.6.2
[13] R.oo_1.7.5 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.12.2
> traceback()
13: readCdfCellIndices(pathname, ...)
12: getCellIndicesChunk(getPathname(this), units = unitsChunk, ...,
verbose = verbose)
11: fcn(idxs[ii], ...)
10: lapplyInChunks.numeric(units, function(unitsChunk) {
cdfChunk <- getCellIndicesChunk(getPathname(this), units =
unitsChunk,
..., verbose = verbose)
res <- vector("list", length(unitsChunk))
res[[1]] <- unlist(cdfChunk, use.names = useNames)
res
}, chunkSize = 1e+05, useNames = useNames, verbose = verbose)
9: lapplyInChunks(units, function(unitsChunk) {
cdfChunk <- getCellIndicesChunk(getPathname(this), units =
unitsChunk,
..., verbose = verbose)
res <- vector("list", length(unitsChunk))
res[[1]] <- unlist(cdfChunk, use.names = useNames)
res
}, chunkSize = 1e+05, useNames = useNames, verbose = verbose)
8: getCellIndices.AffymetrixCdfFile(cdf, units = subset, useNames =
FALSE,
unlist = TRUE)
7: getCellIndices(cdf, units = subset, useNames = FALSE, unlist =
TRUE)
6: getSubsetToAvg.AllelicCrosstalkCalibration(this)
5: getSubsetToAvg(this)
4: getParameters.AllelicCrosstalkCalibration(this)
3: getParameters(this)
2: process.AllelicCrosstalkCalibration(acc2, verbose = verbose)
1: process(acc2, verbose = verbose)
If somebody have a solution.
Thanks you on advance
--
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