Date: Wed, 11 Jul 2007 18:02:04 +0100
From: Wolfgang Huber <huber at ebi.ac.uk>
Subject: Re: [Bioc-devel] [BioC] Peculiar behaviour of
normalize.quantiles (in affy, preprocessCore) if there are NA data
To: Seth Falcon <sfalcon at fhcrc.org>
Cc: bioc-devel <bioc-devel at stat.math.ethz.ch>
Message-ID: <46950D0C.8050301 at ebi.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
Hi Seth & Ben,
thanks for your clarifying comments!
[moved to bioc-devel, where this should have started I think]
Sorry if I have been stepping on feet... the reason for posting to the
bioc user list was that more than once I have (sadly) seen people
looking at histogrammes such as that of qx shown in my previous post,
and using the suggested "cutoff" e.g. to discriminate between expressed
and un-expressed genes, and the like. I hope that this does not sound to
presumptuous, but I think it is a good thing to educate users to
critically assess such results.
Btw, normalizeQuantiles from the limma package appears to deal with NA
values more gracefully (but it is written in R, hence slower). I think
it assumes that the missingness mechanism is random.