[BioC] limit the number of rows in decideTests

[Martin Morgan]

On 06/09/2011 08:20 PM, Wendy Qiao wrote:
> 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?

Hi Wendy -- see the help page for valid arguments to decideTests

   ?decideTests

Subset the result like a matrix, results[1:20,]. How will you decide on 
the number '20'? Shouldn't the results reflect some combination of 
p-value and log fold change? Hope that helps

Martin

>
> 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)
>
> 	[[alternative HTML version deleted]]
>
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