[BioC] Using genefilter

[Nathan.Watson-Haigh at csiro.au]

Hi James,

Since I posted, I actually found your affycoretools vignette and this was really nice to see and very well explained as I'd been doing something similar over recent weeks. One feature that would be nice would be to specify the dir that the plots are save to and/or a file prefix so if you run different normalisations, the files don't get overwritten.

RE: vector not array
The documentation for genefilter needs changing as it says:

     It returns an array of logical values
     (suitable for subscripting) of the same length as there are rows
     in 'expr'. For each row of 'expr' the returned value is 'TRUE' if
     the row passed all the filter functions.

Cheers
Nathan

-----Original Message-----
From:	James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent:	Thu 19/06/2008 21:15
To:	Watson-Haigh, Nathan (LI, Rockhampton)
Cc:	bioconductor at stat.math.ethz.ch
Subject:	Re: [BioC] Using genefilter

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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