[BioC] Re: Affy Present Calls

[Eric]

To string this out a little farther- IMHO the "A" call really means at 
least one of two things is true,

1) the difference in intensities between PMs and MMs was not sufficient for 
the algorithm to call it present, and/or
2) the difference between intensities was not consistently in the PM's favor
In other words, signal could be too dim (if you consider PM-MM to be 
signal, or Tukeys biweight of the logs...) and/or probe set did not behave 
in a manner consistent with the algorithm's expectations.

So what would really be nice is if Affy stopped playing 3-card monte with 
the P/A calls and gave us either a reason for each call or two separate 
calls, one for probe set behavior, one for sufficient intensity.

-E

At 07:16 PM 10/9/2003 +0200, you wrote:
>Date: Thu, 9 Oct 2003 09:45:19 -0700 (PDT)
>From: Francois Collin <fcollin at sbcglobal.net>
>Subject: Re: [BioC] Re: Affy Present Calls
>To: Eric <emblal at uky.edu>, bioconductor at stat.math.ethz.ch
>Message-ID: <20031009164519.71449.qmail at web80406.mail.yahoo.com>
>Content-Type: text/plain
>
>Just a couple of comments to add.
>To filter or not to filter will depend on the application.  If your 
>problem is one of classification and you don't care what fragments are 
>used in your classifier function, there is no harm in filtering absent 
>genes.  You will have plenty of genes to select from among the more 
>reproducible, high intensity fragments that are called present all the 
>time.  If you are looking for marker genes, on the other hand, filtering 
>on presence calls may very well hide some relevent markers.
>What is of interest to me is a thorough characterization of probe sets 
>with respect to the relationship between PM and MM and the effect on 
>detection of mRNA molecule.  When is the call even worthy of its name?  To 
>me "call=P" means PMs are greater than MM by some reasonable 
>measure.  When does is "call=P" equivalent to "the mRNA molecule is 
>present"?  I would publish such a report (If I was editor, that is.)
>
>-f

Eric Blalock, PhD
Dept Pharmacology, UKMC
859 323-8033

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