[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]

J.delasHeras at ed.ac.uk a écrit :
> Quoting Benoit Loup <benoit.loup at jouy.inra.fr>:
>
>> 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
>
> Hi Benoit,
>
> I normally create a list with each individual contrast information 
> (the result of 'topTable', not-ordered, so all probesets in teh same 
> order) as a separate component. I like 'topTable' because it gives me 
> all the info I want. Then I merely compile a large table by combining 
> the columns containing first the annotation info, and then the 
> different contrasts data (I normally just export the log2 ratios and 
> adjusted p values at this stage).
> By putting them in a list you can automate the big table generation no 
> matter how many contrasts you have.
> It may not be the most elegant form, but that's what I do.
>
> Jose
>
>
Thanks a lot Jose,
I finally proceeded as you described it, exporting all the contrasts one 
by one and compiling them after in one file.

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