 Hi, there,

I have a question regarding Affy chip data.

We did many expression arrays and used LIMMA to get the differentially
expressed "genes" (control vs treatment).

However I found that some probesets have multiple genes according to Affy
annotation file.

On the other hand, multiple probesets could match to the same gene.
Even more, some probesets matched to the same gene could be regulated in
different way.

So actually what LIMMA gave us is differentially expressed "probesets".

Say we have 500 probesets up-regulated but we indeed want to know how many
"genes" are up-regulated.

I don't know how to reasonably convert the probesets to genes due to the
non-one-to-one relationship.

What's the convention in the microarray field?

Any suggestion would be greatly appreciated.


Richie

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