Hi Henrik,
I am trying to run the script:
options(echo = FALSE,digits=4)
library(aroma.affymetrix)
verbose <- Verbose(threshold=-8, timestamp=TRUE);
dataSet="Gupta_CC"
chipType <- "GenomeWideSNP_6"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
print(cdf)
dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
dsC <- dsList$total;
print(dsC);
and it is crushing with:
20111024 16:05:12| Normalizing set for PCR fragment-length effects...
20111024 16:05:12| Identifying SNP and CN units...
types
1 2 5
621 934968 945826
20111024 16:05:13| subsetToUpdate:
int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
20111024 16:05:13| Identifying SNP and CN units...done
20111024 16:05:13| Retrieving SNP information annotations...
20111024 16:05:13| Defining DChipSnpInformation from chip type...
20111024 16:05:13| Chip type: GenomeWideSNP_6
20111024 16:05:13| Version:
20111024 16:05:13| Located pathname:
20111024 16:05:13| Defining DChipSnpInformation from chip type...done
Error in list(`doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE,
verbose = verbose)` = <environment>, :
[2011-10-24 16:05:13] Exception: Failed to retrieve SNP information
for this chip type: GenomeWideSNP_6
at throw(Exception(...))
at throw.default("Failed to retrieve SNP information for this chip type: ", ch
at throw("Failed to retrieve SNP information for this chip type: ", chipType)
at getSnpInformation.AffymetrixCdfFile(cdf)
at getSnpInformation(cdf)
at process.FragmentLengthNormalization(fln, verbose = verbose)
at process(fln, verbose = verbose)
at doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose)
at doCRMAv2(csR, ..., verbose = verbose)
at doCRMAv2.character(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = ve
at doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose)
Calls: doCRMAv2 ... getSnpInformation.AffymetrixCdfFile -> throw ->
throw.default -> throw -> throw.Exception
20111024 16:05:13| Retrieving SNP information annotations...done
20111024 16:05:13| Normalizing set for PCR fragment-length effects...done
Execution halted
So, it seems to have problem getting info from CDF file. But
print(cdf) looks normal:
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
and the check sum is identical to one posted on the web:
"3fbe0f6e7c8a346105238a3f3d10d4ec"
All my software is up to date. Any clues?
Thanks
Ivan
--
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