Both examples are correct usage, but the meanings are different and very much dependent on the context.
If the microarray data is being analyzed, then "of" is used to indicate relation.
To better understand the results, we must perform a principal component analysis of the microarray data.
If the microarray data is the outcome of the analysis, then "for" is used to indicate attempting to obtain, gain, or acquire.
We suspected the flux capacitor might contain microarray data, so we decided to perform a principal component analysis (of the flux capacitor to search) for it.
Where "it" is the microarray data.
Another pair of simpler examples:
If we seek the maguffin, then we might
search his luggage for the maguffin
If we suspect kryptonite is hidden within the maguffin, then we might
Perform a search of the maguffin seeking kryptonite