Question: How to merge microarray and RNA-SEQ expression data for DEG analysis?
0
gravatar for ahmad mousavi
14 months ago by
ahmad mousavi470
Royan Institute, Tehran, Iran
ahmad mousavi470 wrote:

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.

rna-seq microarray expression • 725 views
ADD COMMENTlink modified 14 months ago by Kevin Blighe54k • written 14 months ago by ahmad mousavi470
3
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

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:

d

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

Kevin

ADD COMMENTlink modified 14 months ago • written 14 months ago by Kevin Blighe54k
1

thanks a lot, Kevin.

ADD REPLYlink written 14 months ago by ahmad mousavi470
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