Hi, I had successfully analyzed Nimblegen microarray data with oligo package, according to the document, http://www.bioconductor.org/packages/2.4/bioc/vignettes/oligo/inst/doc /oligoNimblegenExpression.pdf . However, I was not able to get normalized data for each probe since the 'rma' funcation returned expression data for each gene summarized via median polish. How can I get the normalized data for each probe before summarizing? Thanks for any help, Tae-Ho Lee -- Tae-Ho Lee Research scientist GreenGene Biotech Inc. Namdong 38-2, Myongji Univ. RM2125 Yongin, Kynggido Korea 449-728 TEL: +82-31-330-6193 FAX: +82-31-321-6355 Email: thlee@ggbio.com alfalf@gmail.net URL:http://www.ggbio.com [[alternative HTML version deleted]]

Tae-Ho Lee wrote: > Hi, > > I had successfully analyzed Nimblegen microarray data with oligo package, > according to the document, > http://www.bioconductor.org/packages/2.4/bioc/vignettes/oligo/inst/d oc/oligoNimblegenExpression.pdf > . > However, I was not able to get normalized data for each probe since the > 'rma' funcation returned expression data for each gene summarized via median > polish. > How can I get the normalized data for each probe before summarizing? > > Thanks for any help, > > Tae-Ho Lee > The general idea to do it is to extract your probe-level matrix with the accessor method "exprs()", then call the method "normalize.quantiles()" from the package "preprocessCore" (eventually after calling "rma.background.correct()" from the same package). Note that you may have to extract the control probes out (others can correct me here, but I am remembering that oligo is removing controls prior to processing). L. -- - Laurent Gautier, Ph.D. Building 301, CBS - Technical University of Denmark DK-2800 Lyngby Phone: +45 45 25 61 45 Fax: +45 45 93 15 85