
Dear BioC,

  According to R documentation for toptable function, the parameter lfc doesn't seem be available for topTableF. Does this mean if I am to use toptableF to view DE genes for a set of contrasts, I am not able to filter genes based on their log-fold change?

 

  Also, on a related note, under p.adjust argument, in the description for "BH" method, it said this method controls FDR to be below a specified value. How do I find out what value this is taking by default, and also, how would I go about changing it?

 

Thank you!

Sincerely,

Casper
 		 	   		  
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