I am working on NCI-60 database for data mining purpose. In NCBI I found miRNA expression profiles ([link][1]). But for mRNA of each cell lines I found 2 kinds of expression profile array in NCBI ([link][2]) categorized as Affymetrix HG-U133A and HG-U133B. They also overlap many mRNA probes and their expression values. I can't understand which one to use or how? What is the difference?

 [1]: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26375
 [2]: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5720
[This PDF][1] from Affymetrix clarifies the difference between 133A, 133 B and 133 plus. As for using the datasets, look at this question: https://www.biostars.org/p/56657/. It seems 60 samples are analyzed using both the chips.

Copy/pasted from Affymetrix website:

> The HG-U133A Array includes representation of the RefSeq database sequences and probe sets related to sequences previously represented on the Human Genome U95Av2 Array. The HG-U133B Array contains primarily probe sets representing EST clusters.

 [1]: http://media.affymetrix.com/support/technical/datasheets/human_datasheet.pdf