RPPA data analysis

Question

[imrankhanbioinfo]

hi, Are there any specific packages to analyze RPPA data?. How about using limma or DeSeq2 for differentially expressed protein analyses? Anyone like to share their experience related to RPPA. Thank you! Imran

Answer 1

[Kevin Blighe]

Hi, I would use limma. RPPA is not count-based data; so, DESeq2 is not appropriate. Even a standard Student's t-test may be fine.

As always, check the distribution of the data that you have in order to better decide which test is appropriate. If you are unsure, consult a statistician.

Also note my previous answer, here: A: Normalizing RPPA data counts from TCGA

Kevin