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List: r-help
Subject: Re: [R] topTable function from LIMMA
From: M Perez <perezperezmm () yahoo ! es>
Date: 2007-02-28 15:04:33
Message-ID: 187690.89702.qm () web25507 ! mail ! ukl ! yahoo ! com
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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@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@ars.usda.gov
> <mailto:roger.vallejo@ars.usda.gov>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained,
> reproducible code.
>
______________________________________________
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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