[BioC] how to generate a data frame containing all the coefficients of the different contrasts, the p-value and the adjusted p-value ?

[Benoit Loup]

Hi to all,

I have a microarray experiment with 10 different contrasts and I would 
like to generate a dataframe containing all the informations exported 
with the function toptable for all the the genes (no restrictions on 
p-value and logFC but with BH adjustment).

For 1 specific contrast I proceed like that :
res=toptable(coef=1,number=15120,fit=fit2,genelist=Ebgnorm$genes[isGene,],adjust.method="BH",A=fit2$Amean,eb=fit2)
res.summary=data.frame(res$ProbeUID,res$ProbeName,res$GeneName,res$Description,res$P.Value,res$adj.P.Val,res$logFC,exp(res$logFC*log(2)))

and after I add to this dataframe the normalized log intensities and 
weights:
lg=data.frame(Ebgnorm$genes$ProbeUID[isGene],Ebgnorm$genes$ProbeName[isGene],Ebgnorm$E[isGene,],Ebgnorm$weights[isGene,])
res2=res.summary[order(res.summary$ProbeUID),]
lg2=lg[order(lg$ProbeUID),]
res2=cbind(res2,lg2[,3:18])
write.table(res2,file="result_Weights_and_Intensities.txt",sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)

It works very well for one contrast but now, I would like to do that for 
all the contrasts at the same time.
I tried the functions write.fit and topTableF but, with the first one I 
cannot have the adjusted p-values and for the second one, there is only 
one column of adjusted p-value (with method="separate" and "global") and 
not one for each contrast.

So, is there any other function to solve my problem or will I have to 
perform the exportation of all contrasts one by one and then concatenate 
them ?

Thank in advance for your help.

Benoit

-- 
Benoit Loup, PhD
UMR Biologie du Développement et Reproduction
Différenciation des Gonades et Perturbations
INRA – Domaine de Vilvert
Bâtiment Jacques Poly
78350 Jouy en Josas
France

Tel: 33 1 34 65 25 38
Fax: 33 1 34 65 22 41
E-mail: benoit.loup at jouy.inra.fr