[BioC] Re: Detection calls - non-Affy (was "loged data or not loged")

[Wolfgang Huber]

Hi Naomi,

> But absent calls are also problematic for other arrays.  E.g. if the 
> transcript is absent, the P(FG>BG) should be close to .5 and so the spot 
> will be flagged about 1/2 the time.  But if the transcript is present 
> for one condition and absent for the other, surely this is highly 
> important - not flagged.
> 
> How are peope handling this?

Here's another reference, which supports the sequential approach (first 
preprocessing, then the "higher-level analysis"). Basically the 
recommendation is to modify the log-ratios so that "generalized 
log-ratios" are shrunken towards 0 if the numbers involved are small but 
coincide with the usual log-ratio if they are large. "small" and "large" 
are automatically defined in terms of the background noise. This allows 
all genes in an experiment to be treated in a uniformly consistent 
manner, without the need for flagging small values.

http://www.ebi.ac.uk/huber/docs/hvhv.pdf (§3), and also
Bioinformatics. 2002;18 Suppl 1:S96-104. PMID: 12169536

There are also a number of papers by David Rocke and Blythe Durbin about 
this.

-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber