[BioC] data reduction in "hist" function?

[Hinnerk Boriss]

Hi Wolfgang!

>  length(which(is.na(exprs(Mydata.rma))))

returns: 0
 
>  length(which(!is.na(exprs(Mydata.rma))))

returns: 128322 which is just three times sum(Mydata.rma.hist$counts) =
42774. 

Why???? Does that help?

Best,
Hinnerk

> 
> 
> Hi all!
> 
> Can someone explain to my why the hist function applied to the
> expression values returns less values, i.e. less genes, than there are
> on the hu68 chip?  
> 
> Here my code fragments:
> 
> > Mydata <- ReadAffy(CDFfile="hu6800.cdf",...)
> > Mydata.rma <- express(Mydata)
> > dim(exprs(Mydata.rma))
> [1] 7129   18
> # ok, here we have 7129 expression values
> 
> > Mydata.rma.hist <- hist(exprs(Mydata.rma),,plot=F)
> > sum(Mydata.rma.hist$counts)
> [1] 42774
> # here we are down to 42774 genes
> 
> Cheers,
> Hinnerk
> 
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