Hi,
sorry to hear you're having these problems. It look rather odd to me,
but usually it turns out to be a very simple cause/solution. Together
with your previous message, it looks like there are some problems with
the annotation data and they may be related or even the same problem.
TROUBLESHOOTING:
If you run these commands, what is the output you get (cut'n'paste):
cdf <- getCdf(csR);
gi <- getGenomeInformation(cdf);
print(gi);
print(getChecksum(gi));
subset <- getUnitsOnChromosomes(gi, 23:24, .checkArgs=FALSE);
str(subset);
/Henrik
On Thu, Mar 3, 2011 at 6:23 AM, Emilie_Sohier <emilie.soh...@gmail.com> wrote:
> 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
>
> --
> 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
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