Ahh. Good to know. I will restart R and give it a try. Thanks! On Thursday, June 14, 2012 4:54:43 PM UTC-4, Henrik Bengtsson wrote: > > > > 1) I have been working from your page. > > http://aroma-project.org/vignettes/CalMaTe - over the course of the > last > > couple of days. I have been following that carefully.. > > > On Thu, Jun 14, 2012 at 12:59 PM, MH <[email protected]> wrote: > >> More or less the complete script follows.. > >> > >> dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose); > >> print(dsList); > >> > >> cmt <- CalMaTeCalibration(dsList); > >> print(cmt); > >> > >> > >> sampleName <- "2_S7_CD15_SNP6"; > >> > >> > >> patientIDs <- c(1,2,4); > >> sampleTypes <- c("tumor", "normal"); > >> > >> pids <- rep(patientIDs, each=length(sampleTypes)); > >> types <- rep(sampleTypes, times=length(patientIDs)); > >> > >> mat <- cbind(names, pids, types); > >> str(mat); > >> > >> idxsN <- which(mat[, "types"] == "normal"); > >> > >> > >> cmtN <- CalMaTeCalibration(dsList, tags=c("*", "normalReferences"), > >> references=idxsN); > > > > > 2) > print(cmtN); > > CalMaTeCalibration: > > Data sets (2): > > <Total>: > > AromaUnitTotalCnBinarySet: > > Name: CLLtest > > Tags: ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > > Full name: CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > > Number of files: 6 > > Names: 1_S7_CD3_SNP6, 2_S7_CD15_SNP6, 3_S7_CD19_SNP6, ..., > 6_S29_CD19_SNP6 > > [6] > > Path (to the first file): > > totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6 > > Total file size: 43.06 MB > > RAM: 0.01MB > > <FracB>: > > AromaUnitFracBCnBinarySet: > > Name: CLLtest > > Tags: ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > > Full name: CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > > Number of files: 6 > > Names: 1_S7_CD3_SNP6, 2_S7_CD15_SNP6, 3_S7_CD19_SNP6, ..., > 6_S29_CD19_SNP6 > > [6] > > Path (to the first file): > > totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6 > > Total file size: 43.06 MB > > RAM: 0.00MB > > Number of arrays: 6 > > Number of references: 3 (50.00%) > > Additional parameters: [2] references: int [1:3] 2 4 6, flavor: chr "v2" > > > > 3) > sessionInfo() > > R version 2.14.2 (2012-02-29) > > 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] preprocessCore_1.16.0 BiocInstaller_1.2.1 sfit_0.1.9 > > calmate_0.9.2 > > [5] MASS_7.3-17 aroma.affymetrix_2.5.0 affxparser_1.26.4 > > aroma.apd_0.2.2 > > [9] R.huge_0.3.0 aroma.core_2.5.0 aroma.light_1.24.0 > > matrixStats_0.5.0 > > [13] R.rsp_0.7.5 R.cache_0.6.2 R.filesets_1.1.5 > > digest_0.5.2 > > [17] R.utils_1.12.1 R.oo_1.9.3 R.methodsS3_1.2.2 > > > > loaded via a namespace (and not attached): > > [1] splines_2.14.2 tools_2.14.2 > > All of the above looks good. FYI, all methods of the Aroma framework > are designed to use a constant amount of memory regardless of chip > type and number of samples, so it's a bit weird that you "run out of > memory" (or more likely, the memory allocated for/by R is so > fragmented that it cannot allocate a continuous stretch of 95.4 > Mbytes). Also, the above script is run part of the regular system > tests and there we don't run out of memory, but I'll check the memory > usage on my Windows 7 machine when I have time. Regardless, I don't > think it is possible troubleshoot this further. > > The good thing though, you can just restart with a fresh R session, > rerun your script and things should go well. Since aroma stores > intermediate and final results to the file system, any steps that have > already been processed will already be there so it should be really > quick to rerun it. Let us know if that works. > > Best, > > Henrik > > > > > thanks, M > > > > > > On Thursday, June 14, 2012 2:31:02 PM UTC-4, Henrik Bengtsson wrote: > >> > >> > >> > Hi All, > >> > I have my test run almost completed and at the step > >> > dsCNList <- process(cmtN, verbose=verbose); > >> > I get the following memory error > >> > Error: cannot allocate vector of size 95.4 Mb > >> > > >> > I am on Windows7, 32bit and have many Gs of storage. > >> > > >> > Any ideas for how to deal with this? > >> > >> My best guess now is that you have done lots of other things in the > >> same R session before doing your aroma analysis, but it is impossible > >> to tell based on that single line of code. So, please post (1) your > >> complete script (at least up to the point where you get the error), > >> (2) the output of print(cmtN), (3) the output of sessionInfo() after > >> you get the error. > >> > >> /Henrik > >> > >> > thanks, M > >> > > >> > -- > >> > 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 > [email protected] > >> > 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 [email protected] > > 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
