Question: How to merge different microarray data sets from different platforms (not for differential expression analysis)?
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gravatar for Moni
3.0 years 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 3.0 years ago by Jean-Karim Heriche23k • written 3.0 years ago by Moni70
1
gravatar for Kevin Blighe
3.0 years ago by
Kevin Blighe65k
Kevin Blighe65k 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 'ArrayVersion' as a covariate in downstream modeling.

Also take a look at my answer here:

Kevin

ADD COMMENTlink modified 9 months ago • written 3.0 years ago by Kevin Blighe65k
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