On Jun 28, 2011, at 5:34 AM, suman pal wrote:
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
You seem to be missing a data object. A google search produces this as
the third hit that suggest you are attempting to run outdate ... well
it is 7 years old ... code:
http://www.rforge.net/bin/results/compton/2.1/data/annotation/hgu95av2-00check.html
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.
This would seem a natural question for the BoConductor mailing list...
after you do a bit more basic searching.
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