Hi,
first thing to try whenever running out of memory in R is to retry in
a fresh R session. That often solves the problem. It's also useful
to know that all your aroma analysis is automatically stored on your
file system, so when you restart aroma will quickly skip the step you
did before.
If restarting does not do it, you can adjust the relative amount of
RAM that some of the aroma pipeline steps are using. Default is 1.0.
By setting it to 0.5, those steps will process the data in chunks with
about half the number of items. By setting it to 10.0, it will
process things in chunks that have 10 times more items. So, if
restarting didn't do it, try adding the following at the top of your
script.
setRam(aromaSettings, 0.5);
Did this solve it?
/Henrik
On Mon, Nov 26, 2012 at 7:36 PM, zhouzaiwei <zhouzai...@163.com> wrote:
> 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!!
>
>
>
> --
> View this message in context:
> http://aroma-affymetrix.967894.n3.nabble.com/Error-cannot-allocate-vector-of-size-618-0-Mb-tp4024959.html
> Sent from the aroma.affymetrix mailing list archive at Nabble.com.
>
> --
> 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.
>
>
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--
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/
