[BioC] Can't reproduce assessment data included in affycomp package

[Philippe Serhal]

I can't quite seem to reproduce the precomputed MAS 5.0 and RMA 
assessments provided in the affycomp package.  Although I have been 
unable to find the code that was originally used to generate them, I 
think it is fairly safe to assume it looked a little something like this 
(given a current working directory containing the HG-U133A spike-in data 
[1]):

R> library (affy)
R> library (affycomp)
R> data <- ReadAffy ()
R> eset <- rma (data)
R> write.table (data.frame (2 ^ exprs (eset), check.names = F),
  + file = "tmp.csv", sep = ",", col.names = NA, quote = F)
R> tmp <- read.newspikein ("tmp.csv")
R> a <- assessSpikeIn2 (tmp, method.name = "RMA_testing")

I then compare this with the precomputed assessments:

R> data (rma.assessment2.133)
R> affycompPlot (rma.assessment2.133, a)

Four of the six resulting figures [2] -- 1b, 2b, 4c, and 5e -- show 
identical results for the two assessments, while the other two -- 5c and 
5d -- show significantly diverging results.  Thinking perhaps the 
assessments had been computed using an older version of RMA, I tried 
'bgversion = 1' in the rma() call, but that didn't help.  In fact, this 
doesn't seem to have anything to do with the RMA pipeline, because if I 
repeat the process substituting 'mas5' for 'rma' and 
'mas5.assessment2.133' for 'rma.assessment2.133' (and not 
exponentiating), I obtain similar results: 5c differs, but none of the 
others.

Any idea what I'm doing wrong here?  Thank you in advance for any 
insight you may be able to provide.

R version: 2.10.0
affy version: 1.24.1

[1] HG-U133A spike-in data: 
http://www.biostat.jhsph.edu/~ririzarr/affycomp/hgu133spikein.tgz
[2] affycomp figure definitions: 
http://affycomp.jhsph.edu/AFFY2/comp_form.html#definitions

-- 
Philippe Serhal
Functional and Structural Bioinformatics Lab
Institute for Research in Immunology and Cancer (IRIC)
Université de Montréal