How to merge microarray and RNA-SEQ expression data for DEG analysis?

Question

[ahmad mousavi]

Dear all,

I'm doing a project which I have to use two separate project on GEO, one of them is Agilent array and second is RNA-Seq.

I've searched a lot, but there were no straightforward answer to my question.

Because both condition samples are not available in a single project I have to use different studies.

Is there anyway to do DEG analysis based on these both platform? ( please share your link or code)

Thanks a lot.

Answer 1

[Kevin Blighe]

There is no straightforward answer for this because it is not a recommend procedure. I have provided various answers in relation to this topic:

Microarray and RNA-seq

• Combine microarray and RNA-seq gene expression for differentially expression analysis
• Compare Microarray with RNA-Seq

Microarray and microarray

• A: How to integrate multiple data sets from microarray platform prior meta-analysis
• How to merge different microarray data sets from different platforms (not for differential expression analysis)?

Your best option is to process them independently and then perform a 'meta analysis' of the results. You can also do things like correlate the fold-changes, as I did here with RNA-seq and proteomics:

You could also perform gene enrichment and pathway analysis on the results and then cross-compare.

Kevin

[ahmad mousavi]

thanks a lot, Kevin.