[BioC] Some Genefilter questions

[James W. MacDonald]

Hi Amy,

Amy Mikhail wrote:
> Hi all,
> 
> I am curious to see how they compare too - as soon as I have the
> subsetting and character vector sorted I will try both and let you know
> how it turns out.
> 
> Out of interest  - would it also be possible to carry out the background
> correction on the full dataset, then remove the parasite probesets, then
> normalise? (and how would one separate these functions in expresso or
> AffyPLM, since there is a placeholder for bg.correct but not for
> normalisation?)

Yes, it should be possible. Pretty much all the functions for computing 
expression values (except mas5()) have a 'normalize' and a 'background' 
argument that you can set to FALSE if you don't want to do that step. So 
you could do something like:

abatch <- ReadAffy()
abatch.bg <- bg.correct.rma(abatch)
## subset the cdf and AffyBatch using Ariel and Jenny's code
eset <- rma(abatch.bg, background=FALSE)

Best,

Jim


> 
> Regards,
> Amy
> 
> ---------------------------------------------------------------------------


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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