[BioC] affy to normalize others single chanels...

[Wolfgang Huber]

Hi Marcelo,

Marcelo Luiz de Laia wrote:
> We have a raw data from naylon membrane (cDNA) and we would like to read 
> and normalize it on affy package.
> 
> Anyone do this (read and normalize) in affy package? Is it possible? Is 
> a good idea?

What I have been doing is to read them in simply with the function 
"read.table", collect the different arrays into a matrix, and then use 
the function "vsn" from the package of the same name to normalize the 
data. For comparison, you could also use normalize.quantiles from the 
affy package (it works on matrices).

I don't think the "AffyBatch" class, which is the main data structure of 
the affy package, is terribly useful for nylon membrane data, since 
there are no probe sets. Consider just using the "exprSet" class instead.

Also, with some tweaking the package "arrayMagic" provides functions 
that might be useful for data import, quality control and visualization 
of these data. Unfortunately the documentation largely ignores nylon 
membranes, and you will probably need to make some workarounds, so I'd 
only recommend this if you are fairly comfortable with R.

Good luck with the filters!

-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber