Hi.
On Mon, Nov 26, 2012 at 10:58 PM, zhouzaiwei <zhouzai...@163.com> wrote:
> Hi, by this code "setRam(aromaSettings, 0.5); ", I could proceed to next
> code although there is still some error"cannot allocate vector of size 304.0
> Mb" and warnings
> what do you mean "retry in a fresh R session"?should I store this project to
> hard disc,turn off R and open R again,then load aroma.affymetrix, open saved
> file and carry out the last code 'csN <- process(mn, verbose=verbose)'?
> sorry for this simple question.
My guess is that you have other things stored in your R environment
which is loaded when you restart R (cf. ?save.image). To avoid
loading that the term is to start a fresh R session. That is
typically done from the command line via:
R --vanilla
and your previous data will not be loaded. If you don't know how to
do that, you can instead wipe your by start R as usual and do:
> rm(list=ls(all.names=TRUE))
> gc()
Then rerun all of your aroma script, i.e.
library(aroma.affymetrix)
setRam(aromaSettings, 0.1)
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "Hs_PromPR_v02"
cdf <- AffymetrixCdfFile$byChipType(chipType)
print(cdf)
s <- AffymetrixCelSet$byName("DS", cdf=cdf)
mn <- MatNormalization(s)
csN <- process(mn, verbose=verbose)
I've tested the above, and with RAM=0.1 as above, R will only use
about 700 MB of RAM. If you use RAM=0.5, it will need 1.1GB and with
RAM=1.0 it will use up to 1.7GB of RAM.
How much RAM/memory do you have on your computer?
/Henrik
>
>
>
>
>
>
> At 2012-11-27 13:57:24,"Henrik Bengtsson-4 [via aroma.affymetrix]" <[hidden
> email]> wrote:
>
> Hi,
>
> first thing to try whenever running out of memory in R is to retry in
> a fresh R session. That often solves the problem. It's also useful
> to know that all your aroma analysis is automatically stored on your
> file system, so when you restart aroma will quickly skip the step you
> did before.
>
> If restarting does not do it, you can adjust the relative amount of
> RAM that some of the aroma pipeline steps are using. Default is 1.0.
> By setting it to 0.5, those steps will process the data in chunks with
> about half the number of items. By setting it to 10.0, it will
> process things in chunks that have 10 times more items. So, if
> restarting didn't do it, try adding the following at the top of your
> script.
>
> setRam(aromaSettings, 0.5);
>
> Did this solve it?
>
> /Henrik
>
> On Mon, Nov 26, 2012 at 7:36 PM, zhouzaiwei <[hidden email]> wrote:
>
>> Hello,
>> I am currently trying to analyze data from affymetrix human promoter
>> tiling
>> 1.0 array by MAT with the following code :
>>> library(aroma.affymetrix)
>>
>>> verbose <- Arguments$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:
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>> 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.
>
>
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> ________________________________
> View this message in context: Re:Re: [aroma.affymetrix] Error: cannot
> allocate vector of size 618.0 Mb
>
> Sent from the aroma.affymetrix mailing list archive at Nabble.com.
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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
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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
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