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

ADD COMMENTlink 14 months ago ahmad mousavi • 430 • updated 14 months ago Kevin Blighe 43k
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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

Microarray and microarray

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.


ADD COMMENTlink 14 months ago Kevin Blighe 43k
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thanks a lot, Kevin.

ADD REPLYlink 14 months ago
ahmad mousavi
• 430

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