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Fong Chun Chan
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@fong-chun-chan-4536
Last seen 10.3 years ago
Depends on how you want to do it:
1) Can you combine all the samples and then do differential
expression? I would argue no because even though the U133A probes are
a subset of the U133plus2 probes (I recall reading this), the
U133plus2 uses additional probes in each probesets to measure gene
expression levels. So you would be getting different gene expression
values for each gene depending on the microarray.
2) Can you do differential expression analysis on each microarray
platform by itself, analyze it separately and combine the results? I
think you would probably have more luck and less criticism doing this.
Since they are both microarray platforms made by the same company,
Affymetrix, you can have more confidence in combining the results.
This is different from saying comparing the results from RNA-Seq to
Microarray since you are dealing with two different platforms and
protocols.
Hope that helps!
Fong
