Question: gcRMA on a GeneFeatureSet from Affy MoGene 1.0 ST v1?
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gravatar for Jean Hausser
11.3 years ago by
Jean Hausser20
Jean Hausser20 wrote:
Hi all, I'm trying to analyze Affy Mouse Gene 1.0 ST v1 chips with BioConductor 2.2 and R 2.7.1. I had a pipeline to process the previous affy chips (MOE430, HGU133 Plus 2.0, etc.) using the affy/gcrma/limma trio but this pipeline won't eat the newer Affy Mouse Gene 1.0 ST chips. Thanks to James McDonald's answer to Hyeong-Min on the BioC mailing-list two weeks ago, I could use the pdInfo package to read in the CEL files into R using oligo. But I'm struggling to run the raw data through gcrma. oligo implements RMA but I'd really like to use gcRMA to compute corrected probe-level intensities. More specifically, I'd like gcrma to use the "antagenomic" probes from the MoGene chip when estimating non-specific binding. I first tried the following: library(gcrma) library(oligo) library(pd.mogene.1.0.st.v1) outputDir <- file.path(getwd(), "chipDBI"); gfs <- read.celfiles(expDesign$filename); chipAnnot <- read.table("MoGene-1_0-st-v1.probe.tab", h=T, sep="\t"); bkgProbes <- chipAnnot$Probe.ID[as.character(chipAnnot$category) == "control->bgp->antigenomic"]; eset <- gcrma(gfs, normalize=F, affinity.source="local", NCprobes=bkgProbes); where "MoGene-1_0-st-v1.probe.tab" is the probe annotation table from Affymetrix. The problem is that gcrma expects an "AffyBatch" affy object while I'm providing a "GeneFeatureSet" oligo object. Therefore, I started hacking a gcrma() function that would work with a GeneFeatureSet. But I quickly ran into trouble because gcrma has a lot of sub-functions, many of them calling to pm(), mm() and IndexProbe(), which are AffyBatch methods that are not implemented in GeneFeatureSet. And even in the first step bg.adjust.optical(), I can't figure how to overwrite probe intensities in a GeneFeatureSet. For instance, "exprs(gfs)[1,1] <- 1" says there's no "exprs<-" method for GeneFeatureSets but still, exprs(gfs) does return the probes intensities... I'm starting to think this is either a bone that's too hard for me to eat in a reasonable amount of time (I'm not really that familiar with the BioC classes and object oriented programming in R) or there is a much easier way I don't know about? So does someone maybe already have a version of gcrma that's working with GeneFeatureSet? Or, is it a feature that is planned for the next version of BioC? Thanks in advance! Cheers, -- Jean Hausser +41 61 267 15 73 Zavolan Group, Bioinformatics, Biozentrum, Universit?t Basel
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