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>Affym etrix</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>Affym etrix</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><platform> 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]]

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@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>Affym etrix</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>Affym etrix</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><platform> 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