Regulation factors for genes on Affymetrix microarrays?

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Regulation factors for genes on Affymetrix microarrays?

Postby Ben_Miller » Nov 28 2007 6:54 pm


Affymetrix microarrays are oligonucleotide microarrays and hence sequences are often "spotted" more than once on the microarrays thus covering different sections or segments of a cDNA sequence (I know they are not really spotted but synthesized in situ on the wafer but for simplicity's sake I'll just call it spotting here).

So, in my results I get more than one "regulation" factor for certain genes. For example, I get a factor indicating a 30-fold difference for one spot and a 10-fold difference for another spot. Sometimes, the discrepancies are very high.

If you want to indicate a regulation factor (change in expression) for a gene covered by more than one oligonucleotide sequence on the Affymetrix gene chip, how would you calculate this factor? Would you calculate the arithmetic mean (if there are multiple spots) or would you calculate the overall factor in any other way?

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fold changes of same target, multiple probes

Postby toxlab » Mar 07 2008 3:28 pm

I would personally report both probes separately...if they are altered in the same direction (up or down) and are significant great--pretty firm answer. If one is sig and the other is not, you still have a pretty good case for the directionality.
as a side note, are you electing to include the mismatch probe information when analyzing your data? I am not current on affy's ideas on normalization, but when I was using their chips we elected to not consider the mismatch probe info for normalization (RMA method instead).
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