Indeed. Hope that helped :) Best, Naira -------- Original Message -------- Subject: Re: [BioC] Duplicate probesets in mouse4302 Date: Tue, 3 Feb 2009 17:36:03 +0000 From: Paul Geeleher <paulgeeleher@gmail.com> To: Naira Naouar <nanao at="" psb.vib-ugent.be=""> References: <2402860e0902020928g7afbb08dqb5ccda4a75e3650f at mail.gmail.com> <4988170F.9010802 at psb.ugent.be> Excellent guys, thanks for the explanations and I will indeed try the remapped CDF files. I'm presuming that the gene-consistent file will have a single entry per gene. Thanks, -Paul. On Tue, Feb 3, 2009 at 10:06 AM, Naira Naouar <nanao at="" psb.vib-="" ugent.be=""> wrote: > Hi Paul, > > You should have a look at this paper > http://nar.oxfordjournals.org/cgi/content/full/33/20/e175?ijkey=zaJM V7qU1XANIci&keytype=ref > > > and following website. > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/g enomic_curated_CDF.asp > > Good luck, > Naira > > Paul Geeleher wrote: >> >> I'm analyzing a dataset from a mouse4302 array and I'm interested in >> looking at the expression levels of the various caspases over the 8 >> timepoints of the experiment. The thing is the mouse4302.db annotation >> package seems to, in many cases, map several different probesets to >> the same genename. For example 3 genesets have genename caspase 3; 3 >> genesets are called caspase 9 and there are duplicates for caspases 8, >> 14, 7 and more. >> >> The next problem is that there is in most cases very little >> correlation between the expression levels of the different genesets >> which are meant to represent the same thing. >> >> For example, caspase 3 as approximate average log expression levels of >> 5.2, 9.1 and 10.2 in the different probesets, which seem hugely >> different. There does however seem to be some correlation in the >> change of expression level over the time course. >> >> My question is basically first, why is this the case? And second, how >> should I deal with it to get some idea what is happening biologically? >> >> > > > -- > ================================================================== > Na?ra Naouar > Tel:+32 (0)9 331 38 63 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > nanao at psb.vib-ugent.be http://www.psb .vib-ugent.be > ================================================================== > > -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- ================================================================== Na?ra Naouar Tel:+32 (0)9 331 38 63 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.vib-ugent.be http://www.psb.vib- ugent.be