Question: How to merge different microarray data sets from different platforms (not for differential expression analysis)?
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gravatar for Moni
19 months ago by
Moni70
Moni70 wrote:

How to merge different microarray datasets from different platforms?
How to merge RNA-Seq data with Microarray data?

ADD COMMENTlink modified 19 months ago by Jean-Karim Heriche18k • written 19 months ago by Moni70
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gravatar for Kevin Blighe
19 months ago by
Kevin Blighe41k
London, England
Kevin Blighe41k wrote:

Dear Moni,

I would not recommend the merging of microarray data from different platforms. Neither would I recommend the merging of RNA-seq data with microarray data. These are best analysed independently, followed by a comparison of the results.

If you must do it, I would normalise each dataset independently using the standardised methods for each technology/platform, and then transform each normalised dataset into Z-scores. Then, attempt to merge, but always keeping 'platform' as a covariate in downstream modeling.

Also take a look at my answer here:

Kevin

ADD COMMENTlink modified 6 months ago • written 19 months ago by Kevin Blighe41k
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