Hello list,

I have a general question that concerns using Limma's linear 
modeling, eBayes, and p-value adjustment methods to determine 
cut-offs in reporting numbers of differentially expressed genes. I 
have gone through the archives and know that this has been discussed 
but please read on.

First, I understand all B-values and t/p-values are only to be used 
as a guide.  But I would like to determine a cut-off value using 
either B or p-values to select genes that are possibly significantly 
differentially expressed so that I can do some small tests using 
these genes, (GO over-representation analysis, etc.). So far I was 
using all the genes with a B-value > 0 as significantly 
differentially expressed. And looking through the archives I find 
that Gordon had once said:


>I dont' think there is any such agreement in the microarray literature even
>for p-values. Given all the assumptions, Terry and I are comfortable only
>with using B-statistics and modified p-values to rank genes rather than as
>absolute cut offs. I often use B>0, but only in an informal way. See
>comments in:
>
>Smyth, G. K. (2004). Linear models and empirical Bayes methods for
>assessing differential expression in microarray experiments. Statistical
>Applications in Genetics and Molecular Biology 3, No. 1, Article 3.
>
>Smyth, G. K., Yang, Y.-H., Speed, T. P. (2003). Statistical issues in
>microarray data analysis. In: Functional Genomics: Methods and Protocols,
>M. J. Brownstein and A. B. Khodursky (eds.), Methods in Molecular Biology
>Volume 224, Humana Press, Totowa, NJ, pages 111-136.
>
>Gordon

I went through these articles again and now maybe I am more convinced 
to base a choice on p-values rather than B since they have less prior 
assumptions, but there really are no rules for cut-offs.

In my particular case if adjust my p-values using fdr, the B-value 
becomes negative before the p-value becomes higher than 0.05.  If I 
adjust with holm, the p-value becomes 0.05 when the B-value is about 4.

Since p-values have less assumptions with them than B-values should I 
use then to make a cut-off instead? And if I use the p-values should 
I use the holm adjusted ones since when I use fdr p-values the 
B-value is negative before the p-value reaches 0.05?

Or can I use any cut-off I like as long as I explain myself? What 
would a journal referee say about that? (This is my main question).

Thanks for your thoughts,  Carolyn


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