> -----Original Message----------- Message: 1 Date: Mon, 1 Mar 2004 16:08:45 +0100 From: <arne.muller@aventis.com> Subject: RE: [BioC] AffyPLM To: <naomi@stat.psu.edu>, <fcollin@sbcglobal.net>, <lpp22@cam.ac.uk>, <bioconductor@stat.math.ethz.ch> Message-ID: <c80ecafa2acc1b45be45d133ed660ade010bf15b@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 NB. I read email only twice a day. If an issue is urgent, please phone.