[BioC] What is the FDR set to for the BH method.

[Naomi Altman]

The "adjusted p-value" for the i_th smallest p-value is mp/i  if this 
is less than 1 and greater than the "adjusted p-value" for the (i-1) 
smallest p-value.  It is truncated at 1.0 from above and at the value 
for the (i-1) value below (so that it always increases as p increases).

This is the estimated FDR for the list of genes you obtain if you 
reject all tests with p less than or equal the i_th smallest p-value.

--Naomi


At 12:51 PM 7/3/2013, Cornish, Joseph (NIH/NIAID) [F] wrote:
>Suppose when I write the results of a microarray experiment fit 
>using limma to file. In doing this I decide to adjust the p-values 
>using the BH method for adjusting the p-values. As I understand it, 
>this method assesses the significance of a result assuming some 
>prior rate of false discovery (type 1 error). I read the 1995 paper 
>for the BH method but I am still confused on what exactly determines 
>this rate? Is it done in a parametric way or non-paramterically?
>
>Joseph Cornish
>Post-Bac IRTA
>NIAID EVPS
>
>
>         [[alternative HTML version deleted]]
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