[BioC] RMA question (weighted averages)

Chris Paulse chrispaulse at hotmail.com
Mon Aug 11 12:34:27 MEST 2003

I have a balanced study of one covariate for which I'm interested in 
obtaining weighted averages of logged expression in each category.  The way 
I've done this has been to load the AffyExtensions package and use the 
fitPLM function.  I have assigned one covariate in the phenoData slot of the 
AffyBatch object.  Then, I've fit a linear model incorporating the "Treated" 
phenotypic variable as follows:

>pset <- fitPLM(rawData, model = PM ~ -1 + probes + Treated)
Background correcting
Fitting models
               Treated_FALSE Treated_TRUE
A01157cds_s_at      6.554139     6.414041
A03913cds_s_at      6.672960     6.830663
A04674cds_s_at      6.981677     6.974190
A07543cds_s_at      7.625168     7.578899
A09811cds_s_at      9.921073    10.624879
A16585cds_s_at      6.757033     6.815193
A17753cds_s_at      7.168006     7.178866
A30543cds_s_at      6.286888     7.007486
A44407cds_at        6.846477     6.796786
AA108277_at         5.773114     5.771723

Are the coefficients here weighted averages of log expression?

Chris Paulse

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