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/.
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