[BioC] Lumi: filtering and batch effects (combat)

[Simone de Jong]

Dear List,

Since your responses helped me many times before, I'm posting two more
questions about Lumi:

* Can I filter genes that are below a certain detection pvalue out of my
file to speed up following analyses?  How can I do that, at what stage and
what should be the threshold? 

* I'm suspecting a batch effect in my data. I can work with ComBat, but I've
no idea how to get the adjusted values back into Lumi (a lumibatch) to go on
with transformation and normalization procedures. Any ideas? 

Thanks,
Simone


___________________
Simone de Jong, Msc.
PhD student
The Netherlands