Hello,
I am currently trying to analyze data from affymetrix human promoter tiling
1.0 array by MAT 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>Affymetrix</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>Affymetrix</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!!
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