[BioC] P calls

Tue Mar 18 13:54:05 MET 2003

On Tue, Mar 18, 2003 at 11:17:05AM -0000, Stephen Henderson wrote:
> 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. 

It probably makes sense to look at things at the probe-set level,
or at the chip probe level as you suggest it.
Using the released version of the package, you can implement the ideas
you suggest.
You will have to write your own 'summary'(*) function (refer to the corresponding
vignette for details). This 'summary' could inspired by one included in
the pack. In your function, you will store the 'A' and 'P' (or whatever)
in a sort of "global" vector (you'll need to use 'get' and 'environment' most
probably)...
The next release (or affy-devel > 1.2.2) would let you do it more easily... 

Hopin' it helps,

Laurent

(*) or "pmcorrect" function if the use of MMs is wished

> 
> 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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