[R] topTable function from LIMMA

[M Perez]

Dear Roger,

I think there is no a default value for the FDR in the
toptable funtion. You will get a p-values corrected by
the method you choose(fdr, bh). 

Briefly the shorted list of p-values will give you the
FDR. It is up to you choose what is the estimated
number of false positives you want to have.

HTH
Manuel   


--- "Vallejo, Roger" <Roger.Vallejo at ARS.USDA.GOV>
escribió:

> 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 at ars.usda.gov
> <mailto:roger.vallejo at ars.usda.gov> 
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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