On Mon, Feb 2, 2009 at 12:28 PM, Paul Geeleher <paulgeeleher@gmail.com>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.
>

Hi, Paul.

This is the rule rather than the exception (not in number, but in
principle).  These are different probesets designed against potentially
different transcripts of the same gene.


>
> 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.
>

Keep in mind that the absolute expression level is not at all comparable
between probesets.  For the purposes of comparison, it is only valid and
useful to compare withing a probeset.  There are many reasons for this
including cross-hybridization and probe design issues.

You suggest that a correlation over time exists between probesets; this is a
good thing.  That said, some probesets will NOT show a correlation over time
with other probesets putatively measuring the same gene.  Again, the reasons
for this can be multiple.  It is not that uncommon, either.

Sean

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