[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 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(fit, results=NULL, file, digits=3, adjust="none",
> 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.
>> 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.
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.
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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