[BioC] Using genefilter

[James W. MacDonald]

Hi Nathan,

Nathan.Watson-Haigh at csiro.au wrote:
>  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.

To which function are you referring? I normally use affycoretools from 
within an Sweave document, so I can use a directive there to specify the 
folder to put the pdfs. Because of this it hasn't occurred to me to 
specify any directories. However, I am open to suggestions.

Best,

Jim


>
>  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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>
>