Case and control in microarray/RNA-seq analysis

Question

[mahdijalili]

Hi, Can I use the case samples from a study and the control samples from another study in microarray/RNA-seq analysis? (specially for cross-study analysis with Bioconductor RankProd R package)

Thanks.

Answer 1

[Manvendra Singh]

If they are stable cell lines then I believe Yes, you can use it but if they are patient materials then I doubt.

All you need is robust normalization and RankProd would remove False discoveries., after that cluster them to see if they look different