On Tue, Dec 03, 2002 at 08:54:13AM -0500, Isaac Neuhaus wrote: > Laurent: > > Can you elaborate a bit more? For example, is computeExprSet an internal > function used by express or expresso? I am afraid it is supposed to be the case... however, it seems that express (that was supposed to have this part of its code based on computeExprSet (*)) do not suffer from it (?!?)... may be we shot ourselves in the foot with CVS... L. (*): I just saw that. For consistency (and try to preserve sanityi by avoiding code duplication) 'express' is very likely make use of 'computeExprSet' in the near future

>>>>> "gregory" == Gregory R Warnes <warnes> writes: gregory> Also, which released version, 1.0 or 1.1? IE, how far back is did the bug gregory> go? 1.1. I don't know how far back, though. gregory> -Greg >> -----Original Message----- >> From: Isaac Neuhaus [mailto:isaac.neuhaus@bms.com] >> Sent: Tuesday, December 03, 2002 8:54 AM >> To: Laurent Gautier >> Cc: bioconductor@stat.math.ethz.ch >> Subject: Re: [BioC] important bug fix in the package affy >> >> >> Laurent: >> >> Can you elaborate a bit more? For example, is computeExprSet >> an internal >> function used by express or expresso? >> >> Isaac >> >> Gautier wrote: >> >> > To whom it makes concerned: >> > >> > The released version of the package problem suffered from a >> rather annoying >> > problem in the method 'computeExprSet'. As a result, the >> expression values >> > computed have very good chances to be rather incorrect >> (whatever the method >> > you used). Many thanks to Michael Morley for warning us >> about strange results >> > compared to MAS5.0 (the bug was found while digging that). >> > I would strongly recommend to re-run expression value >> computation with >> > the version 1.1.1 of the package (should appear by >> tomotrrow on the website) >> > if you are currently working with expression data obtained with 1.1. >> > >> > Sorry for the inconvenience. >> > >> > Laurent >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@stat.math.ethz.ch >> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> gregory> LEGAL NOTICE gregory> Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. gregory> _______________________________________________ gregory> Bioconductor mailing list gregory> Bioconductor@stat.math.ethz.ch gregory> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.)