What are the memory requirments when running Bioconductor's Affy package? I have 38 U95a chips and when I try to process the data I get: expresso(Data,widget=TRUE) background correction: rma normalization: quantiles PM/MM correction : pmonly expression values: medianpolish background correcting...Error: cannot allocate vector of size 83200 Kb In addition: Warning message: Reached total allocation of 1024Mb: see help(memory.size) Is this saying that the vector size for each chip is 83Mb? Otherwise, what is going on? In addition, is this a reasonable analysis or is this duplicating the functions used in rma as may be suggested in "Textual description of Affy", pg 14? I don't quite understand from the vignette. Michael Barnes

You are duplicating rma with expresso, so you *may* be able to do the analysis using rma. I am not sure if the memory requirements are significantly different. There are at least two alternatives to what you are doing. First, you can use justRMA to compute the expression values. If you don't have enough memory to hold an AffyBatch and an exprSet in memory at once (which appears to be the case), you will have to remove the AffyBatch first or you will still run out of memory. The other alternative is to use the functions that Laurent Gautier posted to the list about a month ago (affyEnvPtr). They are designed to minimize the amount of memory used by affy. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Michael Barnes" <michael.barnes@cchmc.org> 06/25/03 08:56AM >>> What are the memory requirments when running Bioconductor's Affy package? I have 38 U95a chips and when I try to process the data I get: expresso(Data,widget=TRUE) background correction: rma normalization: quantiles PM/MM correction : pmonly expression values: medianpolish background correcting...Error: cannot allocate vector of size 83200 Kb In addition: Warning message: Reached total allocation of 1024Mb: see help(memory.size) Is this saying that the vector size for each chip is 83Mb? Otherwise, what is going on? In addition, is this a reasonable analysis or is this duplicating the functions used in rma as may be suggested in "Textual description of Affy", pg 14? I don't quite understand from the vignette. Michael Barnes _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Hi, two (and a half) points, please indicate what platform and what version of R you are using - it is hard to give good advice without you giving us some indications it looks like Windows, in that case there is a FAQ that you can look at www.r-project.org) and the mailing list archives have a number of discussions of just this point, please have a look there memory usage with affy (and a few other things) has been an issue, we are trying to address it and I think that things should improve shortly. Manually removing unneeded objects might help as well. Robert On Wed, Jun 25, 2003 at 08:56:12AM -0400, Michael Barnes wrote: > What are the memory requirments when running Bioconductor's Affy > package? I have 38 U95a chips and when I try to process the data I > get: > > expresso(Data,widget=TRUE) > background correction: rma > normalization: quantiles > PM/MM correction : pmonly > expression values: medianpolish > background correcting...Error: cannot allocate vector of size 83200 Kb > In addition: Warning message: > Reached total allocation of 1024Mb: see help(memory.size) > > Is this saying that the vector size for each chip is 83Mb? Otherwise, > what is going on? > > In addition, is this a reasonable analysis or is this duplicating the > functions used in rma as may be suggested in "Textual description of > Affy", pg 14? I don't quite understand from the vignette. > > Michael Barnes > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+