Re:Re: [aroma.affymetrix] Error: cannot allocate vector of size 618.0 Mb
Hi, by this code setRam(aromaSettings, 0.5); , I could proceed to next code although there is still some errorcannot 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. At 2012-11-27 13:57:24,Henrik Bengtsson-4 [via aroma.affymetrix] ml-node+s967894n402496...@n3.nabble.com 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: createdOn20081204 16:42:56 EST/createdOnplatformAffymetrix/platformchipTypeHs_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: createdOn20081204 16:55:16 EST/createdOnplatformAffymetrix/platformchipTypeHs_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: 101 20121126 20:48:55| Fitting chunk #1 of 5... 20121126 20:48:55|Cells: int [1:101] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ... 20121126 20:48:55|Reading design matrix... 20121126 20:48:55| Retrieving design
Re:Re: Re: [aroma.affymetrix] Error: cannot allocate vector of size 618.0 Mb
Great! By your code it works well and never show errors. at the begain of start R, I use code memory.limit() it shows 1535,and memory.limit(T) shows 14, Does that mean i have not load previous data? I have 8G RAM but the 32 bit windows xp OS only recognize 3.25GB. I used to set RAM by code:setOption(aromaSettings, memory/ram, 0.1) , it seems the function is not like setRam(aromaSettings, 0.1) ,what is the difference between them? At 2012-11-28 03:11:25,Henrik Bengtsson-4 [via aroma.affymetrix] ml-node+s967894n4024964...@n3.nabble.com wrote: Hi. On Mon, Nov 26, 2012 at 10:58 PM, zhouzaiwei [hidden email] wrote: Hi, by this code setRam(aromaSettings, 0.5); , I could proceed to next code although there is still some errorcannot 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$byName(DS, cdf=cdf) mn - MatNormalization(s) csN - process(mn, verbose=verbose) 20121126 20:48:51|Normalization data set for probe-sequence effects... 20121126 20:48:51| Locating probe-sequence annotation data... 20121126 20:48:51| Getting AromaCellSequenceFile... 20121126 20:48:51| Locating... 20121126 20:48:51|Chip type: Hs_PromPR_v02 20121126 20:48:51|Number of cells: 4691556 20121126 20:48:51|Locating AromaCellSequenceFile... 20121126 20:48:51| Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs 20121126 20:48:51|Locating AromaCellSequenceFile...done 20121126 20:48:51| Locating...done AromaCellSequenceFile: Name: Hs_PromPR_v02 Tags: Full name: Hs_PromPR_v02 Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs File size: 116.33 MB (121980713 bytes) RAM: 0.00 MB Number of data rows: 4691556 File format: v1 Dimensions: 4691556x26 Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 Footer: createdOn20081204 16:42:56 EST/createdOnplatformAffymetrix/platformchipTypeHs_PromPR_v02/chipType Chip type: Hs_PromPR_v02 Platform
[aroma.affymetrix] error on FIRMAGene
Hi, everyone, I want to use FIRMAGene to analysis differencial splicing of
hugene-1.0-st array ,there is no overlap between Ensembl identifiers from
getUnitNames() and Affymetrix identifiers in 'hgnetaffx'.follows my code:
library(aroma.affymetrix)
library(FIRMAGene)
hgnetaffx -
read.csv(HuGene-1_0-st-v1.na25.hg18.transcript.csv,sep=,,skip=19,header=TRUE,comment.char=,stringsAsFactors=FALSE)
cdf - AffymetrixCdfFile$byChipType('HuGene-1_0-st-v1', tags=Ensembl,exon)
cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_0-st-v1
Filename: HuGene-1_0-st-v1,Ensembl,exon.cdf
File size: 28.51 MB (29891482 bytes)
Chip type: HuGene-1_0-st-v1,Ensembl,exon
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 27901
Cells per unit: 39.51
Number of QC units: 0
u - which(getUnitNames(cdf) %in% hgnetaffx$probeset_id[hgnetaffx$category
== main hgnetaffx$total_probes 7 hgnetaffx$total_probes 200])
u[1:200]
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[42] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[83] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[124] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[165] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA
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_2.7.0 affxparser_1.28.1 aroma.apd_0.2.3
R.huge_0.4.1 aroma.light_1.28.0
[6] aroma.core_2.7.0 matrixStats_0.6.2 R.rsp_0.8.2
R.devices_2.1.3R.cache_0.6.5
[11] R.filesets_1.6.0 digest_0.6.0 R.utils_1.18.0
R.oo_1.10.2FIRMAGene_0.9.7
[16] R.methodsS3_1.4.2
loaded via a namespace (and not attached):
[1] PSCBS_0.30.0
how can i fix it? did i download the wrong version of annotation?I download
the HuGene-1_0-st-v1.na25.hg18.transcript.csv from www.affymetix.com ;and
HuGene-1_0-st-v1.probe.tab from
http://media.affymetrix.com/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip
i can not find probe.tab of na25.
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[aroma.affymetrix] which version cdf should used when apply FIRMAGene
Hi , I want to apply FIRMAGene to analysis differential splicing events of hugene_1.0_st array and have red article (Robinson Speed, 2007) and script(http://bioinf.wehi.edu.au/folders/firmagene/sup3_04feb2010.R),I want to know which version of cdf file should be used?HuGene-1_0-st-v1,r3.cdf or HuGene-1_0-st-v1,Ensembl,exon.cdf or something else? -- View this message in context: http://aroma-affymetrix.967894.n3.nabble.com/which-version-cdf-should-used-when-apply-FIRMAGene-tp4024986.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. 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/
Re:RE: [aroma.affymetrix] how to get differential region after MatSmoothing?
thanks for your kind answer. At 2013-08-15 08:02:48,Dario Strbenac [via aroma.affymetrix] ml-node+s967894n4025139...@n3.nabble.com wrote: Hello, In the Bioconductor package Repitools, there is a function called regionStats. That will do what you need. You can find out more information at http://www.bioconductor.org/packages/release/bioc/html/Repitools.html From: [hidden email] [[hidden email]] on behalf of zhouzaiwei [[hidden email]] Sent: Wednesday, 14 August 2013 19:38 To: [hidden email] Subject: [aroma.affymetrix] how to get differential region after MatSmoothing? hi all, I am using the affy human promoter 1.0 array to analysis differential methylation level between two group. accoording to the vignettes: MAT - Tiling array analysis (Promoter 1.0R), I get the MatSmoothing object:csMS. Although it could be loaded into IGB to visualization by writeSgr(csMS). I still do not know the exact differential region between two group where as the original MAT could generate. Anyone could help me to figure this out? thanks -- View this message in context: http://aroma-affymetrix.967894.n3.nabble.com/how-to-get-differential-region-after-MatSmoothing-tp4025138.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. 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 [hidden email] To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email]. For more options, visit https://groups.google.com/groups/opt_out. -- -- 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 [hidden email] To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email]. For more options, visit https://groups.google.com/groups/opt_out. If you reply to this email, your message will be added to the discussion below: http://aroma-affymetrix.967894.n3.nabble.com/how-to-get-differential-region-after-MatSmoothing-tp4025138p4025139.html To unsubscribe from how to get differential region after MatSmoothing?, click here. NAML -- View this message in context: http://aroma-affymetrix.967894.n3.nabble.com/how-to-get-differential-region-after-MatSmoothing-tp4025138p4025140.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. 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
