Dear all,

In my analysis, I used 2 different microarray platforms (Affymetrix Human Genome U133 Plus 2.0 Array and Affymetrix Human Gene 1.0 ST Array). However, I don't know how to keep only probes that are on both platforms when combine them into one data set before using limma and combat for perform cross-platform normalization and finding batch effect, respectively.

What can I do to gather only probels that are on both platforms?

Any advice and suggestions will be greatly appreciated.

Thank you.