Hello, I've been able to take advantage of CRMAv2 ability to process arrays in parallel, which is great.
However, when I revisit the data to run, say, CBS on different subsets of the samples I encounter a very long data load time. In particular when I open a new R session I basically run the following code: > chipType <- "GenomeWideSNP_6" > dataSet <- "MyData" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full") > csAll <- AffymetrixCelSet$byName(dataSet, cdf=cdf) I then load the normalized results with: > dsC <- doCRMA( csAll, cdf=cdf, combineAlleles=FALSE, verbose=verbose ) This step takes a very long time even though Crosstalk, Base Position, Probe Summarization, and Fragment Length has already been performed on the samples. I get the following output from my R session when I execute the above statement: 20110118 14:54:22| Identifying non-estimated units... 20110118 14:54:22| Getting chip-effect set from data set... 20110118 14:54:22| Retrieving monocell CDF... 20110118 14:54:22| Monocell chip type: GenomeWideSNP_6,Full,monocell 20110118 14:54:22| Locating monocell CDF... 20110118 14:54:22| Pathname: annotationData/chipTypes/ GenomeWideSNP_6/GenomeWideSNP_6,Full,monocell.CDF 20110118 14:54:22| Locating monocell CDF...done 20110118 14:54:22| Retrieving monocell CDF...done 20110118 14:54:22| Retrieving chip-effects from data set... 20110118 14:54:22| Data set: LungAd 20110118 14:54:22| Retrieving chip-effect #1 of 70 (Patient1)... 20110118 14:54:22| Allocating empty chip-effect file... 20110118 14:54:22| Pathname: plmData/Lung,ACC,ra,-XY,+300,AVG, +300,A+B/GenomeWideSNP_6/Patient1,chipEffects.CEL 20110118 14:54:22| Temporary pathname: plmData/Lung,ACC,ra,-XY, +300,AVG,+300,A+B/GenomeWideSNP_6/Patient1,chipEffects.CEL.tmp 20110118 14:54:22| Renaming temporary file... 20110118 14:54:22| Renaming temporary file...done 20110118 14:54:22| Allocating empty chip-effect file...done 20110118 14:54:22| Setting up CnChipEffectFile... 20110118 14:54:22| Pathname: plmData/Lung,ACC,ra,-XY,+300,AVG, +300,A+B/GenomeWideSNP_6/Patient1,chipEffects.CEL 20110118 14:54:23| Setting up CnChipEffectFile...done 20110118 14:54:23| Retrieving chip-effect #1 of 70 (Patient1)...done 20110118 14:54:23| Retrieving chip-effect #2 of 70 (Patient2)... 20110118 14:54:23| Allocating empty chip-effect file... 20110118 14:54:23| Pathname: plmData/Lung,ACC,ra,-XY,+300,AVG, +300,A+B/GenomeWideSNP_6/Patient2,chipEffects.CEL 20110118 14:54:23| Temporary pathname: plmData/LungAd,ACC,ra,-XY, +300,AVG,+300,A+B/GenomeWideSNP_6/Patient2,chipEffects.CEL.tmp 20110118 14:54:23| Renaming temporary file... 20110118 14:54:23| Renaming temporary file...done 20110118 14:54:23| Allocating empty chip-effect file...done 20110118 14:54:23| Setting up CnChipEffectFile... 20110118 14:54:23| Pathname: plmData/LungAd,ACC,ra,-XY,+300,AVG, +300,A+B/GenomeWideSNP_6/Patient2,chipEffects.CEL and it goes on for hours... Once it finishes I then runnings something like this: > dsR <- getAverageFile(dsC$total) > dsT <- extract(dsC$total, subset.of.interest) > cns <- CbsModel( dsT, dsR ) Could anyone give me suggestions of how I could accomplish rerunning CBS for different subsets without having to constantly execute: > dsC <- doCRMA( csAll, cdf=cdf, combineAlleles=FALSE, verbose=verbose ) to load the normalized results? Thanks a bunch in advance! Greg -- 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/
