Hi. On Wed, Jan 19, 2011 at 11:54 PM, Gregory W <greg.d.w...@gmail.com> wrote: > 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...
Yes, but only the first time. Then it should be fairly quick. > > 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? You can grab the 'dsC$total' data set as follows: dataSet <- "Lung"; tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"; chipType <- "GenomeWideSNP_6"; dsT <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType); This is described in the how to 'Setting up an AromaUnitTotalCnBinarySet or an AromaUnitFracBCnBinarySet': http://aroma-project.org/howtos/SetupOfAromaUnitNnnCnBinarySet Then wrap it up in the dsC list as: dsC <- list(); dsC$total <- dsT; Hope this helps. /Henrik > > 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/ > -- 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/
