[R] Interpretation of log odds
Georg Otto
georg.otto at tuebingen.mpg.de
Tue Feb 12 11:45:32 CET 2008
Dear Corinna,
please do post questions related to bioconductor packages directly to
the bioconductor mailing list. You will have a much higher chance to
get a helpful answer.
The B-statistic is explained best explained in the limma user guide
(chapter 10), which comes with the limma package or from
http://www.bioconductor.org/packages/release/bioc/html/limma.html
Hope that helps,
Georg
"Schmitt, Corinna" <Corinna.Schmitt at igb.fraunhofer.de> writes:
> 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?
>
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