[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 benoit.loup at jouy.inra.fr
Thu Mar 25 10:09:06 CET 2010

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 :

and after I add to this dataframe the normalized log intensities and 

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

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

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