An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061207/ a3656d79/attachment.pl

Hi James, See 'justRMA' - this was developed to help with the memory limitation issues. You really should give the codes you used that led to the error message, plus the output of 'sessionInfo()' for us to be able to help you better. For example, the output of 'rma' should only give one value per probeSET, which is composed of 11 probes, in Affy terminology. That you said you are getting 11 lines for each "individual probe" (probeset, I assume?) means that you were not calling the right function. What was the code you used that supposed led to 11 values after 'rma'? Cheers, Jenny At 08:55 AM 12/7/2006, James Anderson wrote: >Hi, > I have about 53 cel files, each one has the size of about 12-13 mega > bytes with 22625 probes. I am using affycoretools to do rma, but it > complains that the maximum size of memory has been reached. My PC is > Windows XP with 2G RAM. Below is the error information. > >Error: cannot allocate vector of size 209906 Kb >In addition: Warning messages: >1: Incompatible phenoData object. Created a new one. > in: read.affybatch(filenames = filenames, phenoData = phenoData) >2: Reached total allocation of 1024Mb: see help(memory.size) >3: Reached total allocation of 1024Mb: see help(memory.size) > >Since RMA is an across sample normalization, and I need to analyze all the >53 samples together, I can not separate them into several pieces and then >do RMA, MAS5 can do that, but the expression value obtained by MAS5 is not >as good as that of RMA. Does anybody know how to solve this problem? In >addition, it seems that the output of rma in affy package (not >affycoretools) has several lines for each individual probe (my case is 11 >lines for each individual probe), while the rma in affycoretools directly >gives the final expression value for each probe, could anybody tell me how >to make the two results from affy and affycoretools comparable with each >other? > >Thanks a lot! > >James > > >--------------------------------- > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Hi, Have you tried Ben Bolstad's RMAExpress do the initial bg and normalisation? This stand-alone works well for big datasets. A Windows exe is available: http://rmaexpress.bmbolstad.com/ a > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > James Anderson > Sent: 07 December 2006 14:56 > To: bioconductor > Subject: [BioC] out of memory problem using affycoretools > > > Hi, > I have about 53 cel files, each one has the size of about > 12-13 mega bytes with 22625 probes. I am using affycoretools > to do rma, but it complains that the maximum size of memory > has been reached. My PC is Windows XP with 2G RAM. Below is > the error information. > > Error: cannot allocate vector of size 209906 Kb > In addition: Warning messages: > 1: Incompatible phenoData object. Created a new one. > in: read.affybatch(filenames = filenames, phenoData = phenoData) > 2: Reached total allocation of 1024Mb: see help(memory.size) > 3: Reached total allocation of 1024Mb: see help(memory.size) > > Since RMA is an across sample normalization, and I need to > analyze all the 53 samples together, I can not separate them > into several pieces and then do RMA, MAS5 can do that, but > the expression value obtained by MAS5 is not as good as that > of RMA. Does anybody know how to solve this problem? In > addition, it seems that the output of rma in affy package > (not affycoretools) has several lines for each individual > probe (my case is 11 lines for each individual probe), while > the rma in affycoretools directly gives the final expression > value for each probe, could anybody tell me how to make the > two results from affy and affycoretools comparable with each other? > > Thanks a lot! > > James > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061208/ cc6d3400/attachment.pl