[BioC] P calls

[Stephen Henderson]

I agree. I was really trying to elicit advice on an alternative. The funny
thing about the MM probes is that if they just removed them Affy could
produce a single chip with U133A and B genes, and we could all use a PM only
algorithm. BUT then they wouldn't get double the money off some labs. 

For practical purposes however I still need to filter some data-- for
computer intensive clustering or learning. So as I said to R. Irizarry
below, I'm not sure whether to try and do this looking at the probe-set
level or at the expression summary level. 

For instance
If not a test of difference from the mean of the specific MM (robust or
whatever), why not a test of difference from all local MM values in that
sector, or a lower quantile thereof?

Stephen


-----Original Message-----
From: Rafael A. Irizarry [mailto:ririzarr at jhsph.edu] 
Sent: Monday, March 17, 2003 3:30 PM
To: Stephen Henderson
Cc: Ben Rubinstein
Subject: RE: [BioC] P calls

i agree that the notion of P and A might make sense. as you suggest, i 
wouldnt trust affy's way of doing this. i know of one other attempt at 
getting to this. im cc-ing ben rubinstein who has been working on this 
problem.

-rafael


On Mon, 17 Mar 2003, Stephen 
Henderson wrote:

> I think that's probably true that vsn and dchip better assign meaningful
> values to data that is essentially instrument noise. I'm still left
> wondering how best to choose a filter that excludes such data. Whilst for
> modeling purposes it maybe nice to keep the noise as it is information, I
> think for many computer intensive tasks it is practically best to remove. 
> 
> I wonder whether the notion of P and A calls is OK but not best
implemented
> under MAS5? Surely it is better to exclude data based upon the probe level
> data rather than the summary value? No?
> 
> -----Original Message-----
> From: Rafael A. Irizarry [mailto:ririzarr at jhsph.edu] 
> Sent: Monday, March 17, 2003 2:34 PM
> To: Stephen Henderson
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] P calls
> 
> in my opinionm the main reason affy uses these is because MAS 5.0 has so
> much noise at "the bottom". if they didnt, all their large fold changes
> would be for genes with low expression. with RMA, what i use, you dont
> have this problem so i dont see the need to throw away information. there
> are other ways to get rid of the "noise" at the bottom: dChip (pm-only)
> and vsn are two exaples.
> 
> There is no designated place to stick them into exprSet. you could create
> another exprSet just for these or since MAS doesnt give SEs,
> you could stick them in the se.exprs slot. a better (but you need to code
> some) solution is to extend the exprSet class to a new class that includes
> a slot for these calls.
> 
> 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?


-----Original Message-----
From: w.huber at dkfz-heidelberg.de [mailto:w.huber at dkfz-heidelberg.de] 
Sent: Tuesday, March 18, 2003 10:28 AM
To: Reinhold Koch
Cc: bioconductor
Subject: Re: [BioC] P calls


Hi,

> 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".

And in many cases that could just mean that the "MM" is in a fact a
perfect match for something else (esp. in complex transcriptomes such as
human).  The findings in the paper below seem to confirm that notion.

Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ,
Scherf, U, Speed, TP (2002) Exploration, Normalization, and Summaries of
High Density Oligonucleotide Array Probe Level Data. Accepted for
publication in Biostatistics.
http://biosun01.biostat.jhsph.edu/~ririzarr/papers/index.html


Best regards
Wolfgang Huber

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