Case and control in microarray/RNA-seq analysis

[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, cross-platform analysis with Bioconductor RankProd R package)
Also Can I integrate the cell line with patient samples?
Thanks.

[mziemann]

Simple answer is no - this is not considered good form to compare have cases and controls from different studies. The differential genes could be due to many technical differences including RNA isolation (quality), library preparation, sequencing quality, bioinformatics pipelines etc. Nevertheless I have done exactly this in my work and have validated the results by qPCR or other methods.