[BioC] P calls

Reinhold Koch reinhold.koch at unibas.ch
Tue Mar 18 10:35:55 MET 2003

Well, some biologists put great value in Affymetrix' presence calls, so
I looked for papers but could only find one by Lemon et al. 2002:
http://bioinformatics.oupjournals.org/cgi/reprint/18/11/1470?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1047461778635_631&stored_search=&FIRSTINDEX=0&volume=18&firstpage=1470&journalcode=bioinfo. They deal with MAS4 predecessors of the current (MAS5) presence calls and conclude via spike-in experiments that these statistics have an error rate around 80%.

In my opinion an "absent" call just means high values of the MM probes
compared to their corresponding PM probes; other than that I could not
detect any difference between genes called "absent" or "present".

Reinhold Koch

Biozentrum Universitaet Basel
reinhold.koch at unibas.ch

On Mon, 17 Mar 2003, Stephen Henderson wrote:

> I'd like to use the Present (P) and Absent (A) calls for some rudimentary
> filtering of data prior to analysis. Is there an appropriate slot for
> inserting P and A calls within the exprSet object? 
> I'd like to garner opinions: Does anyone else use these , think them
> worthwhile, or perhaps use some other surrogate? 

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