Dear aroma.affymetrix users,
I am using fit function for RmaPlm object and I am getting this error:
Error in .subset2(groups, 1) : subscript out of bounds
cdf file was obtained from brainarray website, version 16
here is the code:
>library(aroma.affymetrix)
>verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>hthgu133aCdf <- AffymetrixCdfFile$byChipType("HTHGU133A_Hs_ENTREZG")
>hthgu133aBatch<-AffymetrixCelSet$byName("ConnectivityMap",
cdf=hthgu133aCdf)
>hthgu133aBatch
AffymetrixCelSet:
Name: ConnectivityMap
Tags:
Path: rawData/ConnectivityMap/HTHGU133A_Hs_ENTREZG
Platform: Affymetrix
Chip type: HTHGU133A_Hs_ENTREZG
Number of arrays: 6026
Names: 5500024017802120306174.A01, 5500024017802120306174.A02,
5500024017802120306174.A03, ..., 5500024053146032309538.H12 [6026]
Time period: [not reported if more than 500 arrays]
Total file size: 31816.39MB
RAM: 5.11MB
>bc.hthgu133a<-RmaBackgroundCorrection(hthgu133aBatch)
>hthgu133aBC<-process(bc.hthgu133a, verbose=verbose)
>qn.hthgu133a<-QuantileNormalization(hthgu133aBC, typesToUpdate="pm")
>hthgu133aN<-process(qn.hthgu133a, verbose=verbose)
>hthgu133aN
AffymetrixCelSet:
Name: ConnectivityMap
Tags: RBC,QN
Path: probeData/ConnectivityMap,RBC,QN/HTHGU133A_Hs_ENTREZG
Platform: Affymetrix
Chip type: HTHGU133A_Hs_ENTREZG
Number of arrays: 6026
Names: 5500024017802120306174.A01, 5500024017802120306174.A02,
5500024017802120306174.A03, ..., 5500024053146032309538.H12 [6026]
Time period: [not reported if more than 500 arrays]
Total file size: 31816.39MB
RAM: 5.11MB
>hthgu133aNPlm<-RmaPlm(hthgu133aN)
>hthgu133aNPlmFit<-fit(hthgu133aNPlm, verbose=verbose)
[...]
20121018 15:26:57| Chunk #1 of 1...done
20121018 15:26:57| lapplyInChunks()...done
20121018 15:26:57| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 5894795 314.9 9040660 482.9 9040660 482.9
Vcells 6325253 48.3 10339736 78.9 9309810 71.1
20121018 15:26:58| readUnits.AffymetrixCdfFile(): Updating cache
20121018 15:26:59| Reading CDF cell indices...done
20121018 15:26:59| Extracting first CDF group for each unit...
Error in .subset2(groups, 1) : subscript out of bounds
20121018 15:26:59| Extracting first CDF group for each unit...done
20121018 15:26:59| Chunk #1 of 1...done
20121018 15:26:59| lapplyInChunks()...done
20121018 15:26:59| Identifying CDF units...done
20121018 15:26:59| Identifying non-fitted units in chip-effect file...done
20121018 15:26:59| Identifying non-estimated units...done
20121018 15:26:59|Fitting model of class RmaPlm...done
and then it stops.
here is sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] pl_PL.UTF-8/pl_PL.UTF-8/pl_PL.UTF-8/C/pl_PL.UTF-8/pl_PL.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_2.6.0 affxparser_1.30.0 aroma.apd_0.2.3
R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.6.0
matrixStats_0.5.3 R.rsp_0.8.2
[9] R.cache_0.6.3 R.devices_2.1.1 R.filesets_1.1.5
digest_0.5.2 R.utils_1.16.2 R.oo_1.9.9
R.methodsS3_1.4.2
loaded via a namespace (and not attached):
[1] tools_2.15.1
Thank you for help
Marcin Siatkowski
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