[BioC] RE : Re: question on limma package
drnevich at uiuc.edu
Thu Jul 19 16:36:30 CEST 2007
I don't know about B statistics offhand (I never use them), but the
adjusted p-values are completely dependent on the number of probes
that you analyze together. In fact, "adjusted" refers to the
correction for multiple hypothesis testing, which is what you are
doing when you do a series of linear models on the probes. Check out
?p.adjust and the references in there for details on different
adjustment methods. In limma, the unadjusted p-values are only
slightly affected by the number of other probes analyzed at the same
time, because it uses a Bayesian correction based on the unexplained
variation across all probes.
At 05:27 AM 7/19/2007, William Mifsud wrote:
>Further to the previous questions about cutoffs for DE genes, I was
>wondering to what extent, if at all, do the adjusted (and unadjusted)
>p-values and B statistics depend on the number of probes on the
>array/'present' probes in a particular experiment?
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives:
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at uiuc.edu
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