[BioC] genefilter

aedin culhane aedin.culhane at ucd.ie
Thu Nov 27 19:50:02 MET 2003

Dear BioC,

I would be grateful for your help, I wish to filter genes which are invariant 
across all arrays. 

I have been looking at genefilter. To start with I tried to set a threshold value of 100 
(default of genefilter) across all arrays.

However if you ask for a min value of 100 across all arrays, genefilter return null. I have
24 arrays in an exprs called mas.x1

> a<-genefilter(mas.x1, filterfun(kOverA(24)))
> sum(a)
[1] 0

> a<-genefilter(mas.x1, filterfun(pOverA(1)))
> sum(a)

However if I make an artifical value just less than the count of arrays it returns a gene list.
Am I missing something here?

> a<-genefilter(mas.x1, filterfun(pOverA(.999999)))
> sum(a)
[1] 8950
> a<-genefilter(mas.x1, filterfun(kOverA(23.9)))
> sum(a)
[1] 8950

Thanks for your help in this,

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