Question: affy: adding new probe set definitions and making rma expression summaries
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gravatar for Mette Langaas
14.1 years ago by
Mette Langaas10 wrote:
1) Problem: want to add five probe sets (from existing probes) in hgfocus-array and make expression summaries for all probesets (existing + five new) using rma (medianpolish) 2) Have: AffyBatch object, dsnorm, of normalized probes. ds <- ReadAffy(filenames=paste(celcatalog,celfilenames,sep="")) dsbgcorr <- bg.correct(ds,method="rma") dsnorm <- normalize(dsbgcorr,method="quantiles") 3) Have: definition of the new probesets: hlag <- "211528_x_at" locpm <- unlist(pmindex(ds,hlag)) locmm <- unlist(mmindex(ds,hlag)) # the five new (overlapping...) probsets by redefining the original probesets hlaglocation <- list(HLAG1to7=cbind(pm=locpm[1:7],mm=locmm[1:7]), HLAG8=cbind(pm=locpm[8],mm=locmm[8]), HLAG9=cbind(pm=locpm[9],mm=locmm[9]), HLAG10to11=cbind(pm=locpm[10:11],mm=locmm[10:11]), HLAG9to11=cbind(pm=locpm[9:11],mm=locmm[9:11])) 4) Howto: how is it possible to "computeExprSet" (or related) with method "medianpolish" for the new probesets located as given in hlaglocation together with all the existing probesets in the AffyBatch object dsnorm? I have read through Bioconductor documentation and mail-list-questions about affy, altcdfenvs, and sadly I am not able to understand how to do this :-( I'm running > version _ platform i686-redhat-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 1.1 year 2005 month 06 day 20 language R Your help is greatly appreciated! Best regards Mette -- Mette Langaas Department of Mathematical Sciences Norwegian University of Science and Technology NO-7491 Trondheim, Norway Voice: +47-7359-1697 URL : http://www.math.ntnu.no/~mettela Fax : +47-7359-3524 Email: mette.langaas at math.ntnu.no -- Mette Langaas Department of Mathematical Sciences Norwegian University of Science and Technology NO-7491 Trondheim, Norway Voice: +47-7359-1697 URL : http://www.math.ntnu.no/~mettela Fax : +47-7359-3524 Email: mette.langaas at math.ntnu.no
probe affy altcdfenvs • 416 views
ADD COMMENTlink written 14.1 years ago by Mette Langaas10
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