Hey, thanks for fast help.
Yes, the cdf was downloaded from brainarray project, cdf version 16 from here: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/entrezg.asp I didn't think cdf is corrupted since there was no error while converting the cdf to binary format. So what I did, is that I have downloaded the same cdf once again, removed results from background correction and quantile normalization (left the rawData and annotation Data folders only) and performed the script once again. It is running already over one week and still going, so this error which was the problem didn't occur. Still don't know what was the problem, but it's ok now. Thanks once again, Marcin W dniu czwartek, 18 października 2012 15:45:30 UTC+2 użytkownik MarcinS napisał: > > 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 > > > > > > > > -- 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 "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
