and oligo may be of interest too (if the annotation package isn't online, you'll need to build your own via pdInfoBuilder)... library(oligo) library(ff) cels = list.celfiles() rawData = read.celfiles(cels) rmaData = rma(rawData) ## resFF is a ff object resFF = exprs(rmaData) resFF[1:10, 1:4] ## if you have RAM to store the exprs matrix resMatrix = resFF[] ## save in a tab-file tmp = as.ffdf(resFF) write.table(tmp, file="results.csv", quote=FALSE, sep="\t") same applies for Exon and Gene ST arrays. b On 14 June 2010 21:49, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Noemi, > > Noemi Andor wrote: >> >> Hi, >> >> I have a problem with the loading of an affybatch object from cel- files. I >> have multiple cel files and want to analyze them all together, yet the >> amount of data is to big to be loaded. I am interested only in a subset of >> genes within those cel-files. So I could load the cel-files into 3 or 4 affy >> objects, then read the expression values of the genes of interest and merge >> them again. But if I read them separatly, the background correction wil not >> be global, and I do not know how to read them without background correction: >> >> pd=read.AnnotatedDataFrame("BI_samples_1.txt", header=TRUE, row.names=1) >> a= ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = >> TRUE) >> eset<-rma(a) >> e206123_at<-exprs(eset["206123_at"]) >> ... >> e210684_s_at<-exprs(eset["210684_s_at"]) >> e1<-rbind(e206123_at,..., e210684_s_at) >> >> If I do the same for BI_samples_2.txt the corresponding e2 will not be >> comparable to e1, am I right? >> >> Would be very greatfull for a good solution to my problem? > > You don't mention your OS, so it is more difficult to suggest. Assuming you > don't have access to a computer with more memory, the memory-bounded > solutions are as follows. > > The xps package of Bioconductor. Requires installation of ROOT, but the > maintainer Christian Stratowa is very active and helpful on this list. > > You will need to go here first to get ROOT. > > http://root.cern.ch/drupal/ > > then a simple biocLite("xps") should get you started. > > A non-BioC but still R based choice is aroma.affymetrix. More info can be > found here: > > http://www.aroma-project.org/ > > > If you are on Windows or Linux, you could use RMAexpress, which is a > standalone software to do RMA. > > http://rmaexpress.bmbolstad.com/ > > > Best, > > Jim > > > >> >> best regards, >> >> Noemi >> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > _______________________________________________ > 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 >