[BioC] Using genefilter

[James W. MacDonald]

Hi Nathan,

Nathan.Watson-Haigh at csiro.au wrote:
> I've managed to use genefilter to generate an array of FALSE and TRUE's
> for the affy bovine array I'm working with:
>  
> -- start code --
> # expSet.RNA.RMAqndata is an ExpressionSet object with log2 expression
> values
>  
> f1<-anyNA
> f2<-kOverA(16, log2(100))   # filter out genes with low/no expression
> over all arrays
> ff<-filterfun(f1,f2)
> wh<-genefilter(expSet.RNA.RMAqndata, ff)
> sum(wh)      # number of genes passing the filter
> -- end code --
>  
> I was wondering if someone could shed light on how to use the wh array
> downstream with things such as limma etc.
>   

What you have isn't an array - it's a vector of TRUE/FALSE that you can 
use to subset your ExpressionSet to remove the reporters that don't pass 
the filter.

expSet.RNA.RMAqndata.filtered <- expSet.RNA.RMAqndata[wh,]

And then you use the filtered data with limma, etc.

Best,

Jim
>  
> Thanks
> Nathan
>  
>  
> -------------------------------------------------------------
> Dr. Nathan S. Watson-Haigh        (publish under Haigh, N.S.)
> OCE Post Doctoral Fellow
> CSIRO Livestock Industries
> J M Rendel Laboratory 
> Rockhampton
> QLD 4701                              Tel: +61 (0)7 4923 8121
> Australia                             Fax: +61 (0)7 4923 8222
>
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