Hi
 
 
I'm currently using RMA-preprocessed microarray data to look for
differentially expressed genes. I used Limma (lmFit, contrast.fit, eBayes)
and topTable (adjust='FDR' = Benjamini&Hochberg I think?) and retained the
genes with logFC >2 and adjusted P-value <0.05 (=double filtering I think?),
but this appears not to be such a good idea (cfr. article)? Should I redo
the analysis now? Is it possible to use the methods explained in the article
in R?
 
 
Thanks for helping
 
 
Koen Marien
Master Student Bioscience Engineering: Cell & Gene Biotechnology
Univerity of Ghent (Belgium)
http://bene.vub.ac.be/Personal%20Pages/KM.htm
 
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This strategy is bound to be less efficient, though.
See a recent article on this subject.
 <http://www.biomedcentral.com/1471-2105/10/402>
http://www.biomedcentral.com/1471-2105/10/402
 
-Christos
 
 
Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park, Suite 5350
Woburn, MA 01801
781-938-3844

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