[BioC] Limma then Annaffy?

davidl@unr.nevada.edu davidl at unr.nevada.edu
Thu Dec 29 01:58:21 CET 2005

Hello all,

     Ive been searching the mail archives for about 2 hours without any luck on
finding an answer to this problem.  I was just wondering if there was a way to
take the results that I obtained from limma and plug them into some sort of
annotation package (such as annaffy).  I am using affymetrix moe4302 gene chips
and would like to learn more about the genes limma found to be differentially
expressed between my two groups.  I was able to use multtest and annaffy to
create the html table, but I would really like to use the differentially
expressed genes from limma (the ones you see in topTable, etc.)

     Also, in searching the mail archives, I saw a few emails indicating that
the adjusted p-values and B values found with limma should not be considered
absolutely correct because of assumptions limma makes about normality (or
something along those lines).  Does this mean that it would be wise to use
another package (or another program?) to find p-values for differential
expression?  I would like to find p-values at some point that are meaningful,
to a certain extent, on their own, as opposed to p-values which indicate just
the relative order of differential expression among genes (and aren't
associated with an actual probability of the absence of differential
expression)(that was worded weird, sorry).  If the assumptions about normality
are the problem, is there a wilcoxon type test that would come reccomended as
part of a bioconductor package? I'm interested in using a fdr type adjustment
for deciding my p-value cut-offs.  Is there any concensus as to the best way to
do this right now?

      Basically, Im just really overwhelmed by the variety of analysis methods
that exist right now for microarrays.  I'm sorry if the answer to my first
question is located in a conspicuous place that I happened to miss and I'm very
appreciative of any any help that anyone would like to offer.

Thank you very much,


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