Hi guys,
I am new to the aroma package and today I just followed the instuction on
Henrik et al's Feb 18, 2008 paper and tried my first test run. But I got the
following error message:
Error in list(`process(acc)` = <environment>,
`process.AllelicCrosstalkCalibration(acc)` = <environment>, :
[2011-06-27 11:16:06] Exception: Failed to
retrieve genome information for this chip type: GenomeWideSNP_6
I googled about this error message and found some people had similar error
before. I tried the suggestions like re-downloading the CDF, but it did not
help.
Any suggestion?
Thanks a lot for your help!
Ying
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
> print(getChecksum(cdf))
[1] "3fbe0f6e7c8a346105238a3f3d10d4ec"
> cs<-AffymetrixCelSet$byName("CCLE_Glioma_CN",chipType="GenomeWideSNP_6")
> acc<-AllelicCrosstalkCalibration(cs)
> csC<-process(acc)
Error in list(`process(acc)` = <environment>,
`process.AllelicCrosstalkCalibration(acc)` = <environment>, :
[2011-06-27 11:16:06] Exception: Failed to retrieve genome information for
this chip type: GenomeWideSNP_6
at throw(Exception(...))
at throw.default("Failed to retrieve genome information for this chip
type: ", chipType)
at throw("Failed to retrieve genome information for this chip type: ",
chipType)
at getGenomeInformation.AffymetrixCdfFile(cdf)
at getGenomeInformation(cdf)
at getSubsetToAvg.AllelicCrosstalkCalibration(this)
at getSubsetToAvg(this)
at getParameters.AllelicCrosstalkCalibration(this)
at getParameters(this)
at process.AllelicCrosstalkCalibration(acc)
at process(acc)
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252
LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.cn_0.7.3 aroma.affymetrix_2.1.0 aroma.apd_0.1.8
affxparser_1.24.0
[5] R.huge_0.2.2 aroma.core_2.1.0 aroma.light_1.20.0
matrixStats_0.2.2
[9] R.rsp_0.5.4 R.cache_0.4.2 R.filesets_1.0.2
digest_0.5.0
[13] R.utils_1.7.5 R.oo_1.8.0 R.methodsS3_1.2.1
The following is a list of files in my
annotationData/chipTypes/GenomeWideSNP_6:
> setwd("GenomeWideSNP_6")
> dir()
[1] "AFFX_README-NetAffx-CSV-Files.txt"
"GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl"
[3] "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
"GenomeWideSNP_6,Full,specialSNPs"
[5] "GenomeWideSNP_6,Full.cdf"
"GenomeWideSNP_6,HB20080710.acs"
[7] "GenomeWideSNP_6,na31,annot.csv"
"GenomeWideSNP_6,na31,hg19,HB20110328.ufl"
[9] "GenomeWideSNP_6.birdseed-v2.models"
"GenomeWideSNP_6.birdseed.models"
[11] "GenomeWideSNP_6.brlmm-p.models"
"GenomeWideSNP_6.cdf"
[13] "GenomeWideSNP_6.chrXprobes"
"GenomeWideSNP_6.chrYprobes"
[15] "GenomeWideSNP_6.cif"
"GenomeWideSNP_6.grc"
[17] "GenomeWideSNP_6.psi"
"GenomeWideSNP_6.r2.qca"
[19] "GenomeWideSNP_6.r2.qcc"
"GenomeWideSNP_6.SMD"
[21] "GenomeWideSNP_6.specialSNPs"
"GenomeWideSNP6.na31.offstranderror.tab"
>
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