Just to close this thread here. Problem was solved, cf. aroma thread '[aroma.affymetrix] Error: cannot allocate vector of size 618.0 Mb' [http://goo.gl/amnbC]. /Henrik On Mon, Nov 26, 2012 at 10:16 AM, Wong, Chao-Jen <cwon2 at="" fhcrc.org=""> wrote: > Have you tried the command gc(reset=TRUE)? It seems you have enough RAM but too segment. You can first try gc(reset=TRUE) to reset the maximum space. If it still doesn't work, restart your computer. > > Cheers, > Chao-Jen > > ----- Original Message ----- > From: "???" <zhouzaiwei at="" 163.com=""> > To: bioconductor at r-project.org > Sent: Monday, November 26, 2012 5:39:10 AM > Subject: [BioC] Error: cannot allocate vector of size 618.0 Mb > > Hello, > I am currently trying to analyze data from affymetrix human promoter tiling array with the following code : >> library(aroma.affymetrix) > > >> verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >> chipType <- "Hs_PromPR_v02" >> cdf <- AffymetrixCdfFile$byChipType(chipType) >> print(cdf) > AffymetrixCdfFile: > Path: annotationData/chipTypes/Hs_PromPR_v02 > Filename: Hs_PromPR_v02.cdf > Filesize: 61.95MB > Chip type: Hs_PromPR_v02 > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2166x2166 > Number of cells: 4691556 > Number of units: 23155 > Cells per unit: 202.62 > Number of QC units: 0 >> s <- AffymetrixCelSet$byName("DS", cdf=cdf) >> mn <- MatNormalization(s) > > >> csN <- process(mn, verbose=verbose) > 20121126 20:48:51|Normalization data set for probe-sequence effects... > 20121126 20:48:51| Locating probe-sequence annotation data... > 20121126 20:48:51| Getting AromaCellSequenceFile... > 20121126 20:48:51| Locating... > 20121126 20:48:51| Chip type: Hs_PromPR_v02 > 20121126 20:48:51| Number of cells: 4691556 > 20121126 20:48:51| Locating AromaCellSequenceFile... > 20121126 20:48:51| Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs > 20121126 20:48:51| Locating AromaCellSequenceFile...done > 20121126 20:48:51| Locating...done > AromaCellSequenceFile: > Name: Hs_PromPR_v02 > Tags: > Full name: Hs_PromPR_v02 > Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs > File size: 116.33 MB (121980713 bytes) > RAM: 0.00 MB > Number of data rows: 4691556 > File format: v1 > Dimensions: 4691556x26 > Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw > Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 > Footer: <createdon>20081204 16:42:56 EST</createdon><platform>Aff ymetrix</platform><chiptype>Hs_PromPR_v02</chiptype> > Chip type: Hs_PromPR_v02 > Platform: Affymetrix > 20121126 20:48:51| Getting AromaCellSequenceFile...done > 20121126 20:48:51| Locating probe-sequence annotation data...done > 20121126 20:48:51| Locating match scores annotation data... > 20121126 20:48:51| Locating AromaCellMatchScoreFile... > 20121126 20:48:51| Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm > AromaCellMatchScoreFile: > Name: Hs_PromPR_v02 > Tags: > Full name: Hs_PromPR_v02 > Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm > File size: 4.47 MB (4691738 bytes) > RAM: 0.00 MB > Number of data rows: 4691556 > File format: v1 > Dimensions: 4691556x1 > Column classes: integer > Number of bytes per column: 1 > Footer: <createdon>20081204 16:55:16 EST</createdon><platform>Aff ymetrix</platform><chiptype>Hs_PromPR_v02</chiptype> > Chip type: Hs_PromPR_v02 > Platform: Affymetrix > 20121126 20:48:52| Locating AromaCellMatchScoreFile...done > 20121126 20:48:52| Locating match scores annotation data...done > 20121126 20:48:52| Reading 'non-missing' cells to fit... > 20121126 20:48:54| Cells to fit: > int [1:4200512] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ... > 20121126 20:48:54| Reading 'non-missing' cells to fit...done > 20121126 20:48:54| Normalizing 1 arrays... > 20121126 20:48:54| Path: probeData/DS,MN,lm/Hs_PromPR_v02... > 20121126 20:48:55| Number cells per chunk: 1000001 > 20121126 20:48:55| Fitting chunk #1 of 5... > 20121126 20:48:55| Cells: > int [1:1000001] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ... > 20121126 20:48:55| Reading design matrix... > 20121126 20:48:55| Retrieving design matrix... > 20121126 20:48:55| Cells: > int [1:1000001] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ... > 20121126 20:48:55| Locating probe-sequence annotation data... > 20121126 20:48:55| Getting AromaCellSequenceFile... > AromaCellSequenceFile: > Name: Hs_PromPR_v02 > Tags: > Full name: Hs_PromPR_v02 > Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs > File size: 116.33 MB (121980713 bytes) > RAM: 0.00 MB > Number of data rows: 4691556 > File format: v1 > Dimensions: 4691556x26 > Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw > Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 > Footer: <createdon>20081204 16:42:56 EST</createdon><platfor m="">Affymetrix</platform><chiptype>Hs_PromPR_v02</chiptype> > Chip type: Hs_PromPR_v02 > Platform: Affymetrix > 20121126 20:48:55| Getting AromaCellSequenceFile...done > 20121126 20:48:55| Locating probe-sequence annotation data...done > 20121126 20:48:55| Locating match scores annotation data... > 20121126 20:48:55| Locating match scores annotation data...done > 20121126 20:48:55| Reading sequence matrix... > 20121126 20:48:55| Reading sequence matrix... > 20121126 20:48:55| Reading data frame... > 20121126 20:48:55| Allocating data object... > 20121126 20:48:55| Number of rows: 1000001 > 20121126 20:48:55| Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw > 'data.frame': 1000001 obs. of 25 variables: > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > $ : raw 00 00 00 00 ... > 20121126 20:48:55| Allocating data object...done > 20121126 20:48:55| Reading data... > 20121126 20:48:59| Reading data...done > 20121126 20:48:59| Reading data frame...done > 20121126 20:48:59| Coerce to a character matrix... > 20121126 20:49:00| Coerce to a character matrix...done > 20121126 20:49:00| Reading sequence matrix...done > 20121126 20:49:00| Reading sequence matrix...done > 20121126 20:49:00| Reading match scores... > 20121126 20:49:01| Allocating data object... > 20121126 20:49:01| Number of rows: 1000001 > 20121126 20:49:01| Column classes: integer > 'data.frame': 1000001 obs. of 1 variable: > $ : int 0 0 0 0 0 0 0 0 0 0 ... > 20121126 20:49:01| Allocating data object...done > 20121126 20:49:01| Reading data... > 20121126 20:49:01| Reading data...done > 20121126 20:49:01| Reading match scores...done > 20121126 20:49:01| Constructing design matrix... > Error: cannot allocate vector of size 618.0 Mb > In addition: There were 17 warnings (use warnings() to see them) > 20121126 20:49:08| Constructing design matrix...done > 20121126 20:49:08| Retrieving design matrix...done > 20121126 20:49:08| Reading design matrix...done > 20121126 20:49:08| Fitting chunk #1 of 5...done > 20121126 20:49:08| Path: probeData/DS,MN,lm/Hs_PromPR_v02...done > 20121126 20:49:08| Normalizing 1 arrays...done > 20121126 20:49:08|Normalization data set for probe-sequence effects...done >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) > > > locale: > [1] LC_COLLATE=Chinese_People's Republic of China.936 LC_CTYPE=Chinese_People's Republic of China.936 > [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C > [5] LC_TIME=Chinese_People's Republic of China.936 > > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] aroma.affymetrix_2.6.0 affxparser_1.28.1 aroma.apd_0.2.3 R.huge_0.4.1 aroma.light_1.28.0 > [6] aroma.core_2.6.0 matrixStats_0.6.2 R.rsp_0.8.2 R.cache_0.6.5 R.devices_2.1.3 > [11] R.filesets_1.6.0 digest_0.5.2 R.utils_1.18.0 R.oo_1.10.2 R.methodsS3_1.4.2 > > >> memory.limit() > [1] 1535 >> memory.limit(T) > [1] 1077 > anyone can help me?should i upgrade my pc hardware? Thanks!! > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Chao-Jen Wong > Grady Lab / Clinical Research > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M1-B514 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2 at fhcrc.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor