[BioC] [Fwd: Re: Duplicate probesets in mouse4302]

[Naira Naouar]

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 at 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=zaJMV7qU1XANIci&keytype=ref
>
>
> and following website.
> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_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?
>>
>>
>
>
> --
> ==================================================================
> Naïra 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


-- 
==================================================================
Naïra 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