Hi Suman,
On 6/28/2011 10:02 AM, David Winsemius wrote:
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
As David notes, this question is better asked on the BioC listserv. And
it is really old code. The LOCUSID object has been deprecated for a long
time now, replaced by ENTREZID, and as the warning notes, geneNames()
has been deprecated in favor of featureNames.
So try
ll <- mget(featureNames(esetSel), hgu95av2ENTREZID)
also GOHyperG() is gone as well, replaced by S4 methods that might be a
bit less easy to figure out. I don't have the book you are working
through, but you would be better served if you were to use the vignettes
that come with the packages you are using instead (or at least as a way
to get updated examples of how to use the package).
Anyway, please direct all future questions about BioC packages to the
BioC listserv.
Best,
Jim
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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David Winsemius, MD
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--
James W. MacDonald, M.S.
Biostatistician
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University of Michigan
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