[BioC] RMA normalization and MAS5.0 detection calls - correction

[Jenny Drnevich]

I just noticed that what I wrote before was the opposite of what I meant:

>Actually, the problem of the statistical results not always making sense
>with the P/A calls also happens with MAS5 values, not RMA or GCRMA
>specifically. Many years ago I as using Affy's two sample comparison in the
>MAS 5.0 software, and I noticed that a probeset would be called "A" in
>sample 1 and "P" in sample 2, but supposedly sample 2 had higher expression
>than sample 1!!

It should read sample 1 = A, sample 2 = P, but sample 1 > sample 2. 
Otherwise, why would I think it made no sense? :)

Have a good day!
Jenny




>The calls and the expression level comparisons sometimes
>don't correspond, but this is because they use different algorithms and
>values in their computation, as Jim explained. I tend to like and use the
>calls in a conservative matter, but they may only be about 85% accurate
>(Choe et al. Genome Biology 2005, 6:R16).
>
> >Another way to approach filtering probesets is based on the variability
> >of the probesets over all samples. If the variance is low (below some
> >constant c), then you might assume that the gene is not differentially
> >expressed in any samples (which is different than saying it is expressed
> >or not). These genes are uninteresting by definition, and can be removed
> >from the dataset.
>
>I still haven't convinced myself that I like this approach. And wouldn't it
>be better to filter on CV, which takes into account expression level,
>rather than variance? I know there was a recent exchange on what sort of
>cutoff value to use... I really need to find the time to play around with
>filtering on some aspect of variability - unless something has been
>published on it?
>
>Cheers,
>Jenny
>
>
>
>
> >HTH,
> >
> >Jim
> >
> >
> > >
> > >
> > > Regards!
> > >
> > >
> > > haiyan
> > >
> > >       [[alternative HTML version deleted]]
> > >
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> >
> >--
> >James W. MacDonald, M.S.
> >Biostatistician
> >Affymetrix and cDNA Microarray Core
> >University of Michigan Cancer Center
> >1500 E. Medical Center Drive
> >7410 CCGC
> >Ann Arbor MI 48109
> >734-647-5623
> >
> >
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>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu
>
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