Combine microarray and RNA-seq gene expression for differentially expression analysis

Question

[landscape95]

Hi everyone, I wonder whether we can combine the RNA-seq data with microarray gene expression data together to do the differential expression analysis or others signature scoring methods since as far as I know, microarray is based on image intensity and RNA-seq is based on the counts of mapped reads?

Your help is really appreciated.

[WouterDeCoster]

I wonder whether we can combine the RNA-seq data with microarray data

Question unclear. Do you mean you want to compare dataset A with condition A (using microarray) with dataset B with condition B (using RNA-seq)? Or do you mean that your condition A has both samples quantified using microarray and RNA-seq, and you want to compare that with condition B which also has both microarray and RNA-seq data.

Answer 1

[Kevin Blighe]

I feel that you should conduct the studies independently and then perform a meta-analysis of the results. Take a look at RankProd

[AfinaM]

In case where we might have treatment dataset A (microarray) and control dataset B (RNA-seq), how can we go from this?