Probe sets in Affymetix array

[echristo]

Dear community,

This is the first time that I post a topic so first let me introduce myself.
My name is Eleni and I am doing Bioinformatics research. I have some basic knowledge of Biology but my first degree is Informatics, so some things are not very clear to me...Lately I have been working with microarray data processing, and especially Affymetrix. I knew that each Affymetrix array can have several probes representing the same gene and that these probes' information is summed up to one probe set. What I did not know is that there may exist probe sets on an array which correspond to the same gene. My question is "Which of the probe sets which represent the same gene is better to use for making statistical computations with the specific gene? If all of them contribute to a final value, how is this value calculated?" This is crucial for doing correctly my analysis, but I am lost in Affymetrix sites and data sheets...If someone knows something more about this issue I would be glad to hear!

Thanks a lot for your time,
Eleni

[JackBean]

I think, that if there are more probe sets, they are probably relevant to splicing variants. If not, the response should be the same.