Search
Question: need help regarding quality assessment of raw data
0
gravatar for varshika singh
5.6 years ago by
varshika singh20 wrote:
Dear sir/madam I am using library arrayQualityMetrics for quality assessment of raw data. I used following commands: > library(affy) > dat<-ReadAffy() > library(arrayQualityMetrics) > arrayQualityMetrics(expressionset=dat,outdir="rawreport", + force=TRUE,do.logtransform=TRUE) and it gave error as: Error: cannot allocate vector of size 124.0 Mb when i used the same for processed data i got the result. Kindly help. Varshika Singh PhD Scholar (Banasthali university, India) [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.6 years ago by Steve Lianoglou12k • written 5.6 years ago by varshika singh20
0
gravatar for Steve Lianoglou
5.6 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, On Saturday, January 5, 2013, varshika singh wrote: > Dear sir/madam > I am using library arrayQualityMetrics for quality assessment of raw data. > I used following commands: > > library(affy) > > dat<-ReadAffy() > > library(arrayQualityMetrics) > > arrayQualityMetrics(expressionset=dat,outdir="rawreport", > + force=TRUE,do.logtransform=TRUE) > and it gave error as: > Error: cannot allocate vector of size 124.0 Mb > when i used the same for processed data i got the result. Kindly help. You are running out of RAM. how many arrays are you trying to process? How much ram do you have? Are you running R as 64bit? Also please provide the output of sessionInfo() after you have loaded arrayQualityMetrics -steve Varshika Singh > PhD Scholar > (Banasthali university, India) > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <javascript:;> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]
ADD COMMENTlink written 5.6 years ago by Steve Lianoglou12k
0
gravatar for Steve Lianoglou
5.6 years ago by
Denali
Steve Lianoglou12k wrote:
On Sunday, January 6, 2013, varshika singh wrote: > hi, > I have 3 GB RAM. And the output for sessionInfo() is: > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) Sounds like you need a CPU with more ram -- you never answered how many arrays you are trying to process? -steve > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.14.0 Biobase_2.18.0 > [3] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affy_1.36.0 affyio_1.26.0 affyPLM_1.34.0 > [4] annotate_1.36.0 AnnotationDbi_1.20.3 beadarray_2.8.1 > [7] BeadDataPackR_1.10.0 BiocInstaller_1.8.3 Biostrings_2.26.2 > [10] Cairo_1.5-2 cluster_1.14.3 colorspace_1.2-0 > [13] DBI_0.2-5 gcrma_2.30.0 genefilter_1.40.0 > [16] grid_2.15.2 Hmisc_3.10-1 hwriter_1.3 > [19] IRanges_1.16.4 lattice_0.20-10 latticeExtra_0.6-24 > [22] limma_3.14.3 parallel_2.15.2 plyr_1.8 > [25] preprocessCore_1.20.0 RColorBrewer_1.0-5 reshape2_1.2.2 > [28] RSQLite_0.11.2 setRNG_2011.11-2 splines_2.15.2 > [31] stats4_2.15.2 stringr_0.6.2 survival_2.36-14 > [34] SVGAnnotation_0.93-1 vsn_3.26.0 XML_3.95-0.1 > [37] xtable_1.7-0 zlibbioc_1.4.0 > > On Sun, Jan 6, 2013 at 9:46 PM, Steve Lianoglou < > mailinglist.honeypot@gmail.com <javascript:_e({}, 'cvml',=""> 'mailinglist.honeypot@gmail.com');>> wrote: > >> sessionInfo() > > > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]
ADD COMMENTlink written 5.6 years ago by Steve Lianoglou12k
0
gravatar for Steve Lianoglou
5.6 years ago by
Denali
Steve Lianoglou12k wrote:
Hi Varshika, Please CC the bioc-list so that you can get more eyeballs to help w/ your problem, and any help that you do receive will be useful to others. so: On Tue, Jan 8, 2013 at 11:49 AM, varshika singh <varshika13singh at="" gmail.com=""> wrote: > hi, > size of arrays=1164x1164 features (13 kb) You still haven't answered how many arrays you are trying to process. All signs are pointing to the fact that you do not have enough RAM on your machine -- even if you did it wouldn't help because you are running R in 32bit mode. I'm not sure what other help I can offer other than suggesting you hunt for a larger (more ram) machine to do the arrayQC and normalization steps so that you can hopefully continue w/ downstream analysis on your own machine. I know the aroma suite of tools can process lots of arrays on low ram machines, so you can use that to normalize, but I'm not sure what type of QC reports they generate along the way. Perhaps others may have more useful suggestions, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 5.6 years ago by Steve Lianoglou12k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 146 users visited in the last hour