[BioC] RE: AffyPLM

[Mark Reimers]

> -----Original Message-----------

Message: 1
Date: Mon, 1 Mar 2004 16:08:45 +0100
From: <Arne.Muller at aventis.com>
Subject: RE: [BioC] AffyPLM
To: <naomi at stat.psu.edu>, <fcollin at sbcglobal.net>, <lpp22 at cam.ac.uk>,
	<bioconductor at stat.math.ethz.ch>
Message-ID:
	<C80ECAFA2ACC1B45BE45D133ED660ADE010BF15B at crbsmxsusr04.pharma.aventis.com>

Content-Type: text/plain;	charset="iso-8859-1"

If the horizontal striping (due to the scanner) is a systematic error, then
one doesn't have to bother, right? However, I've found some strange blobs
(with "tentacles") on a few of my chips that sneeked through the standard
QC.
I guess this is not be a systematic error.

How do you decide when you've to discard a chip?

	regards,

	Arne
----------------------------------------------------------------
Arne,
We find that the SE estimates are useful, in conjunction with MDS plots of
samples. When one sample has a much higher SE range than the rest, then that
sample almost always appears as an outlier in the MDS plots. Conversely, the
majority of extreme outliers (but not all) seem to come from chips with high
SE values.

regards

Mark



================
Mark Reimers,
Laboratory of Molecular Pharmacology
National Cancer Institute
Bldg 37, room 5068
Bethesda, MD 20892
+1 301-402-2706
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