[BioC] Re: Detection calls - non-Affy (was "loged data or not
huber at ebi.ac.uk
Mon Apr 4 10:45:12 CEST 2005
> 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
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