[BioC] limma genedata
Dennis Hazelett
hazelett at uoneuro.uoregon.edu
Thu Mar 11 20:22:44 MET 2004
Hello all,
Thankyou for your suggestions yesterday (re: getting started), they were
extremely helpful. Now I have a more specific question about the limma
User's guide. In section 8.2 on the 2-sample w/reference method, the
plot commands reference an object "genelist" that points nowhere for me.
I have to delet the item to get the command to work, and this causes
results to be returned absent identifiers. I'm referring to the
following command:
toptable(coef=2,number=15,genelist=genelist[,1:6],fit=fit,eb=eb,adjust="fdr")
? Can I replace
genelist=genelist[,1:6]
with
genelist=RG$genes
or something similar? It seems to be necessary to get the names of the
genes in the output from Bayes analysis. I am using a non-model organism
with some cDNA libs of my own construction, so only a fraction of the
clones are sequenced and the rest have clone ID's.
By the way, most of the image links in the LIMMA User's Guide are broken.
-Dennis
p.s. I'm working from a debian linux platform.
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