Dear list,

I tried to compare raw summarized expression values coming from miRNA QC
Tool (background detection, RMA global background correction, median polish
summarization) to expresso output using line:

expresso(afbatch=myabatch, bg.correct = TRUE, bgcorrect.method = "rma",
normalize = FALSE, pmcorrect.method = "pmonly",summary.method =
"medianpolish", verbose = TRUE,widget = FALSE)

on the same set of CEL files, but they are quite different. Importing the
same QC Tool cdf file "miRNA-1_0.cdf" in R library led to same results of
standard bioconductor "mirna10cdf". I'm apparently using the same algorithms
(RMA bg correction and median polish), but it seems there is something
different between Affy QC tool processing and expresso procedure. Is this
possible?


Thanks all for any suggestion

Giacomo


Dr Giacomo Tuana
Dipartimento di Scienze Mediche, Università degli Studi di Milano
U.O. Ematologia 1 - CTMO Fondazione IRCCS Ca' Granda Ospedale Maggiore
Policlinico
via Francesco Sforza, 35
20122 MILANO (Italy)
tel. 0255033328

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