Hello,
I basically want to use R-help, and post some problems which I am facing. The Ref is a well known Genome Biology paper "Bioconductor: open software development for computational biology and bioinformatics" by Robert C Gentleman et al., 2004. Generating Heatmaps till Fig2 is working so I think esetSel is not the problem..
However, for generating the Figure 3, for GO annotations the following command is not working:
> ll <- mget(geneNames(esetSel),hgu95av2LOCUSID)   
#it is displaying error messages  Error in mget(geneNames(esetSel), hgu95av2LOCUSID) : object 'hgu95av2LOCUSID' not foundand also geneNames not found try featureNames instead
Hence I cant proceed to the next set of commands provided in the paper which are as follows:
> ll <- unique(unlist(ll))> mf <- as.data.frame(GOHyperG(ll))[, 1:3]> mf <- mf[mf$pvalue < 0.01, ]
sincerelySumanCCMB Hyderabad.

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