[BioC] P calls (VSN and RMA)

[Naomi Altman]

I have also been working on this problem.

I compared the Affy "present" calls, and calls based on various levels of 
normalized expression.  Needless to say, these do not match well.

In our study, it is known that some genes do express at very low levels in 
one of our conditions, and do not express under the other 
conditions.  These genes were declared "not present" in all conditions both 
by Affy and by our (admittedly arbitrary) cut point  (which was 50).

I did a gene-by-gene ANOVA (which included all genes, even if 
"absent").  Interestingly enough, a few of these genes had a statistically 
significant ANOVA F-test and a look at the expression values confirmed that 
this was due to much higher expression  values (2-fold or more) in the 
known condition.  This seemed to me to indicate that perhaps we ought to 
consider lowering the cut point.  However, if we do this, we also include a 
lot more genes that appear (by RT-PCR) to really be absent.

So, now I wonder if I can use the ANOVA to provide information about when a 
gene is present.  I appreciate this discussion, because it is an important 
issue for the group of biologists I work with.

--Naomi

At 04:39 PM 1/9/2004, w.huber at dkfz-heidelberg.de wrote:
>Hi Isaac and Petra,
>
>On Fri, 9 Jan 2004, Isaac Neuhaus wrote:
> > still the biological fact that a lot of the probesets on any chip assay
> > genes that are not expressed in the cell type being tested.
> > Incorporating the null measurements for these probesets greatly affects
> > any kind of multiple test corrections applied in analysis of the data.
>
>The P/A calls from Affymetrix are trying to decide on the presence or
>absence of a gene in a single sample. For the kind of statistical analyses
>you are talking about, genes that are absent in some samples and present
>in others may still be very interesting, maybe the most interesting ones.
>On the other hand side, to reduce the multiple testing problem, it is good
>to throw out genes that never do anything. However, this is necessarily a
>trade-off between false positives and false negatives, and the decision
>should, among other things, involve the costs of false positives and false
>negatives, respectively. In my opinion, the P/A calls are so popular
>mostly because they give a false sense of objectivity and simplicity.
>...but, as I said, that's just an opinion.
>
>Best wishes
>  Wolfgang
>
>
>
>-------------------------------------
>Wolfgang Huber
>Division of Molecular Genome Analysis
>German Cancer Research Center
>Heidelberg, Germany
>Phone: +49 6221 424709
>Fax:   +49 6221 42524709
>Http:  www.dkfz.de/abt0840/whuber
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111