Integration of the TCGA's Agilent 244K and Affymetrix data

Question

[Researcher]

Hello All, Can we integrate the Agilent 244K and Affymetrix data from TCGA? Does anyone has some experience with this and can share any workflow, if there is any?

Thanks

Answer 1

[jared.andrews07]

I highly recommend you don't try this. Integrating two very different platforms is unlikely to go well or be a productive use of your time. You could potentially look at common CN changes identified by each, but trying to integrate them both into a single analysis is best avoided.

edit: OP also received an answer to this in the bioconductor slack regarding the originally mentioned CGH arrays, to which Henrik Bengtsson said you can actually normalize between platforms used for the same samples in a fairly robust manner with the aroma.cn R package, so TIL.

[Researcher]

Hi @jared, Thank you for your kind reply. My question is more about the gene expression, where they share 10779 genes for TCGA-GBM. Would it be recommended to use the expression values from the two in a common matrix and do some batch correction?

Thanks

[jared.andrews07]

Well, CGH arrays (like the 244k array) don't measure gene expression, so I assume you mean some other platforms then. My answer is the same for gene expression. Relative comparisons between platforms is your best best.