[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
Fri Mar 26 16:06:48 CET 2010

Saroj K Mohapatra a écrit :
> Hi Benoit:
>> I tried the functions write.fit and topTableF but, with the first one 
>> I cannot have the adjusted p-values 
> ?write.fit
> ...
> Usage:
>     write.fit(fit, results=NULL, file, digits=3, adjust="none", 
> method="separate",
> F.adjust="none", sep="\t", ...)
> ...
>  adjust: character string specifying multiple-testing adjustment
>          method for the t-statistic P-values, e.g., ‘"BH"’. See
>          ‘p.adjust’ for the available options. If ‘NULL’ or ‘"none"’
>          then the P-values are not adjusted.
> It seems if you change the adjust parameter from "none", you should be 
> able to get what you want.
> Best,
> Saroj
>> 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 Saroj,
When I tried the function "write.fit",  I  specified adjust="BH" and 
method="separate" but when I opened my file I did not see any "adjust 
p.value" column header but "t.statsitic". In fact, I did not well see 
and I was wrong... I apologise for this mistake.
Thanks a lot.

Best regards.


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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