[R] Interpretation of log odds

From: Schmitt, Corinna <Corinna.Schmitt_at_igb.fraunhofer.de>
Date: Mon, 11 Feb 2008 20:05:33 +0100

Hallo,

> fit12<-lmFit(qrg[,1:2])
> t12<-toptable(fit12,adjust="fdr",number=15000,genelist=qrg$genes[,1])
> t12

            ID     logFC         t              P.Value                        adj.P.Val                        B
1560	orf6.2714  -5,95911144	-7,504537362	0,0000000000000616459272630    0,0000000000430961073320568	20,85141454
8689	SW23	    2,709344216	 3,41198098	0,0006449261297639210000000    0,0396758555030764000000000	-0,62704052


The data example comes from one experiment, where I want to know if genes are differentially expressed. As I saw in the onlinehelp for toptable the value B is the log odds that the gene is differentially expressed. When I now look at the B value 20,85141454 it says that the gene orf6.2714 is in 20,85% differentially expressed. Is it right? But how should I interpret the second example SW23 with a negative B value?

Can anyone discribe it to me in easy word? ;-)

Thanks, Corinna

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