[BioC] affymetrix miRNA QC Tool vs expresso data discrepancy

[James W. MacDonald]

Hi Giacomo,

On 3/2/2011 12:23 PM, Giacomo Tuana wrote:
> 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?

Of course. The algorithms have been implemented by two different groups, 
one of which isn't known for releasing complete details of their 
algorithms. So what you think you are doing with the miRNA QCTool may 
not in fact be what you are doing.

In addition, I don't see an 'rma' style background correction for the 
miRNA QCTool in their user manual. It appears they are using a 
gcrma-type background correction.

Best,

Jim


>
>
> 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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>
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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