questioning about PCA graph in RNASeq analysis

Question

[Alaa]

i want to ask something about PCA graph i get from DESEQ2 analysis .....is it necessary that the two groups im comparing show difference or can they be inteergreted together like the dots of for example healthy group should in in a place and dots of diseased group should be in another place ....or can they show the same pattern?

[Arup Ghosh]

Given that the samples were not interchanged or cross-contaminated, the overlap between case and control samples in the PCA suggests that the treatment or perturbation has little or no influence on gene expression.

[Alaa]

But this means I still can get statistically important results or not ?even with bad PCA Because the core is to combine multiple studies different platforms some give good PCA some not

[Arup Ghosh]

If you are combining multiple studies using different platforms, I would suggest checking for and correcting batch effects before DE analysis.