Dear R-Help,

 

I am using the function "topTable" from the LIMMA package.  To estimate
adjusted P-values there are several options (adjust="fdr" , adjust="BH")
as shown below:

 

topTable(fit, number = 10, adjust = "BH", fit$Name)   

 

I guess any of these options (fdr, BH, etc.) is using a default of
FDR=0.05 which is quite conservative (i.e., very likely none of the
tested genes will be ranked as differentially expressed at 5% FDR). I
would argue that for an exploratory study it would be okay to use a 0.05
< FDR <0.20. So, I was wondering if we can change that default of
FDR=0.0.5 with a less stringent FDR value (0.10, 0.20, etc.) in the
"topTable" function.  How do I change it?

 

Thanks a lot for the help on the use of "topTable" function from the
LIMMA package.

 

Roger

 

 

Roger L. Vallejo, Ph.D.

Computational Biologist & Geneticist

U.S. Department of Agriculture, ARS          

National Center for Cool & Cold Water Aquaculture

11861 Leetown Road

Kearneysville, WV 25430

Voice:    (304) 724-8340 Ext. 2141

Email:   roger.vallejo@ars.usda.gov <mailto:roger.vallejo@ars.usda.gov> 

 


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