[BioC] Limma: correct calculation of B statistics (log odds)

[Wittner, Ben, Ph.D.]

Jose,

I'm very glad you asked this question. One of the things that has made me wary
of using limma is that the proportion of differentially expressed genes is often
one of the primary things I'm trying to discover from the data, so I feel uneasy
making an assumption as to what that proportion is. In your email below, you say
that the output of limma is sensitive to the assumption, which, of course, makes
me feel even more uneasy about it.

I've not noticed any responses on the BioC list. Has anyone commented on this
issue to you?

-Ben

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-
> bounces at stat.math.ethz.ch] On Behalf Of J.delasHeras at ed.ac.uk
> Sent: Wednesday, April 19, 2006 8:06 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Limma: correct calculation of B statistics (log odds)
> 
> 
> I have been using B values to rank genes in order of more likely to
> less likely (differentially expressed) in LimmaGUI.
> 
> I am now using Limma, I noticed the default value for the parameter
> "proportion" (on the function eBayes) is set at 0.01 (expected 1%
> differentially expressed genes). I didn't pay much attention to this
> parameter before, because in LimmaGUI you cannot specify it.
> 
> However, now that I use "straight" Limma more I was playing with the
> proportion parameter and it affects the B stats a lot. Therefore I come
> to the question of what's the best way to estimate this parameter.
> 
> My first guess is to use the P values (FDR, calculated by BH) to decide
> a cut off, usually 0.05. Then see how many genes are differentially
> expressed according to that rule. And use this observed proportion of
> differentially expressed genes as my proportion parameter.
> 
> Is this the correct way to do it?
> 
> Jose
> 
> --
> Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
> The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
> Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
> Swann Building, Mayfield Road
> University of Edinburgh
> Edinburgh EH9 3JR
> UK
> 
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