[BioC] RE : Re: question on limma package

[Richard Friedman]

Dear El Mouselly,

	B is the log odds score that the genes are differentially  expressed.
	if odds>1 that the genes are differentially expressed is a cutoff  
then B=log odds>0 is the cutoff.
	According to  Gordon Smyth the author of Limma (and Gordon  please  
correct me if I am wrong)
the B>0  cutoff is recommended over p-value cutoffs. If you wish to  
use a p-value cutoff then
you can either correct for fmultiple tests by using p<.001 or by  
correcting the p-value in some way
(I use Benjamin-Hochberg false discoveries) and use p-corrected<.05.
By validation by pcr I mean checking by pcr if  genes with B>0 are  
indeed differentially expressed.
I hope that this helps. I can send you my course powerpoint slides on  
this subject off list if you are interested.

Best wishes,
Rich



On Jul 18, 2007, at 10:49 AM, el mousselly antra wrote:

> dear friedman,
> i have not well understand , my question
> is when i obtain the list  list of p-value of different genes  
> (after executing limma)
> i don't know if i consdier all genes that they have p-value < 0.05  
> are differentially expresed or
> butor we take a number very small than 0.05 in order to obtain  
> minimum of genes differentially expressd in the result butmore  
> reliable .
> in you response i don't undertand
> i have not undersytand a b <f 0 and also the validation by pcr
> thank you
> sincerly
> Richard Friedman <friedman at cancercenter.columbia.edu> a écrit :
> Dear Mouselly,
>
> A B>f 0 is a good place to start.
> It is advisable to spot check genes by PCR to validate the cutoff.
>
> Best wishes,
> Rich
>
> On Jul 18, 2007, at 10:06 AM, el mousselly antra wrote:
>
> > hi,
> > i have a question on limma package
> > when we have the result of tnis pakage and we have p-vlue and the
> > value of B .
> > i i want to know on wich value of p we consider that genes are DE ,
> > we take 0.05 is the threshold or what and i see that when we  
> consider
> > 0.05 as threshold wa have a lot of genes DE.
> > so, i want some rule (threshold)that will be raisonnable and
> > efficient to detect gnes DE
> > thank you
> > sincerly
> >
> >
> >
> >
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> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Biomedical Informatics Shared Resource
> Lecturer
> Department of Biomedical Informatics
> Educational Coordinator
> Center for Computational Biology and Bioinformatics
> National Center for Multiscale Analysis of Genomic Networks
> Box 95, Room 130BB or P&S 1-420C
> Columbia University Medical Center
> 630 W. 168th St.
> New York, NY 10032
> (212)305-6901 (5-6901) (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> In memoriam, John Stewart Williamson
>
>
>
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------------------------------------------------------------
Richard A. Friedman, PhD
Biomedical Informatics Shared Resource
Lecturer
Department of Biomedical Informatics
Educational Coordinator
Center for Computational Biology and Bioinformatics
National Center for Multiscale Analysis of Genomic Networks
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, John Stewart Williamson