Can't reproduce assessment data included in affycomp package
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@philippe-serhal-4602
Last seen 9.6 years ago
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) Universit? de Montr?al
Cancer affycomp PROcess safe Cancer affycomp PROcess safe • 863 views
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