[BioC] RMA + loess normalisation and filtering

[Wolfgang Huber]

Hi again,


>> question 1: I have performed *RMA normalisation *of my Affymetrix 
>> data. However, for further analysis I think it is necessary to 
>> *filter* the data (non-expressed genes or below background). However I 
>> don't know the best way to filter the genes that are not expressed or 
>> very low expressed (below the background), based on the RMA 
>> normalisation data.
> 
> 
> My preference is to select genes based on their overall variability, 
> using a criterions such as
> 
>    z = apply(exprs(x), 1, IQR)



Just remembered - a discussion (with data) on whether to select on mean 
level or variability can be found here:

http://www.bepress.com/bioconductor/paper7/

There are also additional ideas on pre-filtering, in order to alleviate 
the loss of power from multiple testing.

-- 
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