[BioC] More than one weight with marrayRaw class

Gordon Smyth smyth at wehi.edu.au
Wed Nov 12 00:54:27 MET 2003

At 01:44 AM 12/11/2003, Mike Schaffer wrote:
>Using marrayRaw, Is there a way to combine two columns of data from a 
>GenePix file into the Weight for a spot?
>For instance I would like to read in the "Flag" and "F Pixels" columns 
>from the GenePix file to filter out all flagged spots and spots below a 
>threshold size.  It doesn't appear this is possible without modifying the 
>marray classes.

read.maimages() in the limma package provides a way to do this. Simply 
define your own custom function mywtfun() which takes a data frame argument 
and computes the weights as you want, then use

RG <- read.maimages(files, source="genepix", wt.fun=mywtfun)

Converting the RGList object back to an marrayRaw object is pretty easy, if 
that's what you want to do, but you'd have to do it yourself.



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