[BioC] Affymetrix question

Jenny Drnevich drnevich at uiuc.edu
Wed Oct 26 17:28:03 CEST 2005

At 07:54 AM 10/26/2005, you wrote:
>lucia García wrote:
> > Hello,
> > I have a question for the analysis of microarays data in affymetrix. It is
> > possible to use the Detection Call (P/A/M) with obtained data with RMA,
> > Thank you
>You *could* use the detection calls with these methods, but I am not
>sure if it would be informative or not. First, these calls don't really
>tell you if the gene is 'present' or not - all they do is tell you if
>the expression of the PM probes appears to be greater than that of the
>MM probes. Given that 30 - 40% of the MM probes are larger than the PMs,
>the utility of the detection calls is questionable.

There is a paper by Choe et al. 2005 
(http://genomebiology.com/2005/6/2/R16) where they created another spike-in 
experiment, except that they derived all the RNAs by PCR; they spiked-in 
about 1300 RNAs at different concentrations and used another ~2500 RNAs at 
equal concentrations as the background RNA population. As far as I'm aware, 
this experiment is unique in that they "knew" all the RNAs that were 
present, and according to their analysis the P/A/M detection call was 
pretty accurate. I don't use MAS5, but I do pre-filter the genes based on 
P/A/M calls in a very conservative way: only if a gene called absent in all 
chips is it thrown out.

That's my 2-cents,

>Second, the only method you mention that uses the MM probe data is MBEI
>(and only if you use the PM-MM model). If you are not using the MM probe
>data, how useful is it to know that the PMs are larger than the MMs?
>If you are simply trying to remove those genes that appear not to be
>expressed, then you might look at some of the functions in the
>genefilter package, as well as this paper (particularly section 2.1).
> >
> > _________________________________________________________________
> > Descubre la descarga digital con MSN Music. Más de medio millón de
> > canciones. http://music.msn.es/
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>James W. MacDonald
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

More information about the Bioconductor mailing list