That worked and I got up and running again. However, I just hit another error at extract signal. I have included the command before it also.
> print(dsCNList); $total AromaUnitTotalCnBinarySet: Name: CLLtest Tags: ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY,CMTN,v2,normalReferences Full name: CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY,CMTN,v2,normalReferences 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,CMTN,v2,normalReferences/GenomeWideSNP_6 Total file size: 43.06 MB RAM: 0.01MB $fracB AromaUnitFracBCnBinarySet: Name: CLLtest Tags: ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY,CMTN,v2,normalReferences Full name: CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY,CMTN,v2,normalReferences Number of files: 6 Names: 1_S7_CD3_SNP6, 2_S7_CD15_SNP6, 3_S7_CD19_SNP6, ..., 6_S29_CD19_SNP6 [6] Path (to the first file): totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY,CMTN,v2,normalReferences/GenomeWideSNP_6 Total file size: 43.06 MB RAM: 0.00MB > extractSignals <- function(dsList, sampleName, reference=c("none", "median"), refIdxs=NULL, ..., verbose=FALSE) { + reference <- match.arg(reference); + idx <- indexOf(dsList$total, sampleName); + dfT <- getFile(dsList$total, idx); + dfB <- getFile(dsList$fracB, idx); + tcn <- extractRawCopyNumbers(dfT, logBase=NULL, ..., verbose=verbose); + baf <- extractRawAlleleBFractions(dfB, ..., verbose=verbose); + if (reference == "median") { + if (!is.null(refIdxs)) { + dsR <- extract(dsList$total, refIdxs); + } else { + dsR <- dsList$total; + } + dfTR <- getAverageFile(dsR, verbose=verbose); + tcnR <- extractRawCopyNumbers(dfTR, logBase=NULL, ..., verbose=verbose); + tcn <- divideBy(tcn, tcnR); + tcn$y <- 2*tcn$y; + } + list(tcn=tcn, baf=baf); + } > pch <- 19; > cex <- 0.8; > > snT <- sampleName; > chr <- 8; > > for (normalRefs in c(TRUE, FALSE)) { + if (normalRefs) { + figName <- sprintf("%s,Chr%02d,CalMaTe,normalReferences", snT, chr); + dataT <- extractSignals(dsList, sampleName=snT, chromosome=chr, reference="median", refIdxs=idxsN, verbose=verbose); + dataTC <- extractSignals(dsCNList, sampleName=snT, chromosome=chr, verbose=verbose); + } else { + figName <- sprintf("%s,Chr%02d,CalMaTe", snT, chr); + dataT <- extractSignals(dsList, sampleName=snT, chromosome=chr, reference="median", verbose=verbose); + dataTC <- extractSignals(dsCList, sampleName=snT, chromosome=chr, verbose=verbose); + } + + + toPNG(figName, width=1200, { # (save to figures/) + subplots(4, ncol=1); + par(mar=c(2,5,1,1)+0.1, cex=cex, cex.lab=2.4, cex.axis=2.2); + + plot(dataT$tcn, ylim=c(0,4), pch=pch); + plot(dataT$baf, pch=pch); + plot(dataTC$tcn, ylim=c(0,4), pch=pch); + plot(dataTC$baf, pch=pch); + }); + } Extracting RawCopyNumbers object... Name: 2_S7_CD15_SNP6,total Chromosome: 8 Identifying units on chromosome... AromaUgpFile: Name: GenomeWideSNP_6 Tags: Full,na31,hg19,HB20110328 Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp File size: 8.97 MB (9407867 bytes) RAM: 0.00 MB Number of data rows: 1881415 File format: v1 Dimensions: 1881415x2 Column classes: integer, integer Number of bytes per column: 1, 4 Footer: <createdOn>20110328 19:16:46 PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><createdBy><fullname>Henrik Bengtsson</fullname><email>h...@aroma-project.org</email></createdBy><srcFiles><srcFile1><filename>GenomeWideSNP_6,Full.CDF</filename><filesize>493291745</filesize><checksum>3fbe0f6e7c8a346105238a3f3d10d4ec</checksum></srcFile1><srcFile2><filename>GenomeWideSNP_6.na31.annot.csv</filename><filesize>1501563495</filesize><checksum>3f59efe386ffc1af656d01be0ab035e9</checksum></srcFile2><srcFile3><filename>GenomeWideSNP_6.cn.na31.annot.csv</filename><filesize>879257480</filesize><checksum>6a21fef62c71fb56bc5dda4499b70a7f</checksum></srcFile3></srcFiles> Chip type: GenomeWideSNP_6,Full Platform: Affymetrix Units: int [1:98308] 55161 55162 55163 55164 55165 55166 55167 55168 55169 55170 ... Genomic positions: int [1:98308] 190568 237498 239189 239324 281424 281572 282252 282384 415401 446359 ... Identifying units on chromosome...done Extracting data... num [1:98308] 2748 5059 5300 2567 1878 ... Extracting data...done Extracting RawCopyNumbers object...done Extracting RawAlleleBFractions object... Name: 2_S7_CD15_SNP6,fracB Chromosome: 8 Identifying units on chromosome... AromaUgpFile: Name: GenomeWideSNP_6 Tags: Full,na31,hg19,HB20110328 Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp File size: 8.97 MB (9407867 bytes) RAM: 0.00 MB Number of data rows: 1881415 File format: v1 Dimensions: 1881415x2 Column classes: integer, integer Number of bytes per column: 1, 4 Footer: <createdOn>20110328 19:16:46 PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><createdBy><fullname>Henrik Bengtsson</fullname><email>h...@aroma-project.org</email></createdBy><srcFiles><srcFile1><filename>GenomeWideSNP_6,Full.CDF</filename><filesize>493291745</filesize><checksum>3fbe0f6e7c8a346105238a3f3d10d4ec</checksum></srcFile1><srcFile2><filename>GenomeWideSNP_6.na31.annot.csv</filename><filesize>1501563495</filesize><checksum>3f59efe386ffc1af656d01be0ab035e9</checksum></srcFile2><srcFile3><filename>GenomeWideSNP_6.cn.na31.annot.csv</filename><filesize>879257480</filesize><checksum>6a21fef62c71fb56bc5dda4499b70a7f</checksum></srcFile3></srcFiles> Chip type: GenomeWideSNP_6,Full Platform: Affymetrix Units: int [1:98308] 55161 55162 55163 55164 55165 55166 55167 55168 55169 55170 ... Genomic positions: int [1:98308] 190568 237498 239189 239324 281424 281572 282252 282384 415401 446359 ... Identifying units on chromosome...done Extracting data... num [1:98308] 1 0.226 0.182 0.118 0.571 ... Extracting data...done Extracting RawAlleleBFractions object...done Retrieving average unit signals across 3 arrays... Searching for an existing file... Paths: [1] "totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6" Filename: .average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb Searching path #1 of 1... Path: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6 Pathname: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb Searching path #1 of 1...done Located pathname: Searching for an existing file...done Allocating empty data file to store average signals... Path: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6 Filename: .average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb Adding temporary suffix from file... Pathname: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb Suffix: .tmp Rename existing file?: FALSE Temporary pathname: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb.tmp Adding temporary suffix from file...done Dropping temporary suffix from file... Temporary pathname: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb.tmp Suffix: .tmp Regular expression for suffix: \.tmp$ Pathname: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb Renaming existing file... Result: TRUE Renaming existing file...done Dropping temporary suffix from file...done Allocating empty data file to store average signals...done AromaUnitTotalCnBinaryFile: Name: .average-signals-median-mad Tags: 65e3f541c6c39dfbe63b1428b7c795f5 Full name: .average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5 Pathname: totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5.asb File size: 7.18 MB (7525849 bytes) RAM: 0.00 MB Number of data rows: 1881415 File format: v1 Dimensions: 1881415x1 Column classes: double Number of bytes per column: 4 Footer: <createdOn>20120615 11:06:00 EDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType> Platform: Affymetrix Chip type: GenomeWideSNP_6,Full Number of units to be updated: 1881415 Processing chunk... chr "Indices in chunk:" int [1:1881415] 1 2 3 4 5 6 7 8 9 10 ... Reading data... Reading data...done Estimating averages and standard deviations... Estimating averages and standard deviations...done Writing estimates... Writing estimates...done Processing chunk...done Retrieving average unit signals across 3 arrays...done Extracting RawCopyNumbers object... Name: .average-signals-median-mad,65e3f541c6c39dfbe63b1428b7c795f5 Chromosome: 8 Identifying units on chromosome... AromaUgpFile: Name: GenomeWideSNP_6 Tags: Full,na31,hg19,HB20110328 Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp File size: 8.97 MB (9407867 bytes) RAM: 0.00 MB Number of data rows: 1881415 File format: v1 Dimensions: 1881415x2 Column classes: integer, integer Number of bytes per column: 1, 4 Footer: <createdOn>20110328 19:16:46 PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><createdBy><fullname>Henrik Bengtsson</fullname><email>h...@aroma-project.org</email></createdBy><srcFiles><srcFile1><filename>GenomeWideSNP_6,Full.CDF</filename><filesize>493291745</filesize><checksum>3fbe0f6e7c8a346105238a3f3d10d4ec</checksum></srcFile1><srcFile2><filename>GenomeWideSNP_6.na31.annot.csv</filename><filesize>1501563495</filesize><checksum>3f59efe386ffc1af656d01be0ab035e9</checksum></srcFile2><srcFile3><filename>GenomeWideSNP_6.cn.na31.annot.csv</filename><filesize>879257480</filesize><checksum>6a21fef62c71fb56bc5dda4499b70a7f</checksum></srcFile3></srcFiles> Chip type: GenomeWideSNP_6,Full Platform: Affymetrix Units: int [1:98308] 55161 55162 55163 55164 55165 55166 55167 55168 55169 55170 ... Genomic positions: int [1:98308] 190568 237498 239189 239324 281424 281572 282252 282384 415401 446359 ... Identifying units on chromosome...done Extracting data... num [1:98308] 2924 3757 5788 2567 2177 ... Extracting data...done Extracting RawCopyNumbers object...done Error in value[[3L]](cond) : [2012-06-15 11:06:24] Exception: Failed assign column 'y', because: replacement has 0 rows, data has 98308 at #09. value[[3L]](cond) - value[[3L]]() is local of the calling function at #08. tryCatchOne(expr, names, parentenv, handlers[[1L]]) - tryCatchOne() is local of the calling function at #07. tryCatchList(expr, classes, parentenv, handlers) - tryCatchList() is local of the calling function at #06. tryCatch({ this <- NextMethod("[[<-", this) }, error = function(ex) { msg <- sprintf("Failed assign column '%s', because: %s", name, ex$message) throw(msg) }) - tryCatch() is in environment 'base' at #05. `[[<-.RichDataFrame`(`*tmp*`, name, value = numeric(0)) - `[[<-.RichDataFrame`() is in environment 'aroma.core' at #04. `[[<-`(`*tmp*`, name, value = numeric(0)) - `[[<-`() is local of the calling function at #03. `$ 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 <mha...@broadinstitute.org> 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 > 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/ > -- 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/