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

[Saroj K Mohapatra]

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
>