[BioC] limit the number of rows in decideTests

Gordon K Smyth smyth at wehi.EDU.AU
Sat Jun 11 02:21:19 CEST 2011

Dear Wendy,

decideTests() tells you which genes satisfy chosen criteria for each 
contrast in your design.  It does not limit the number of hits in advance, 
and there is no way to do this.  It does not rank genes.

If you want only a fixed number of top probes, you must use topTable(), 
which is designed to do this.

Best wishes

> Date: Thu, 9 Jun 2011 23:20:10 -0400
> From: Wendy Qiao <wendy2.qiao at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] limit the number of rows in decideTests
> Dear all,
> I have a data set consisted of 4 cell types with each cell type having 3
> replicates. I find the unique signature genes of each cell types using
> decideTests (see following). I only want the top, say 20 signature probes
> that satisfy my thresholds.  I tried to use "number=20" as for the
> "topTable" function with "decideTests", but it gave me the an error (see
> below). Is there a way that I can define the number of upregulated probes
> for outputting in decideTests?
> Thank you in advance,
> Wendy
> Code:
> results <- decideTests(fit[,-1], p=0.10, lfc=log2(2),number=20)
> Error in decideTests(fit[, -1], p = pval, lfc = log2(foldchange), number =
> 20) :
>  unused argument(s) (number = 20)

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