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Validate RNAseq Models in Microarray Data?

Hi,

I built a risk score model for trying to predict melanoma outcomes in TCGA-SKCM, based in FPKM data from the patients (I know of the drawbacks of using FPKM, but this is more of a test).

I was looking at the literature and very frequently, the risk score (when built in TCGA cohort) is also validated in microarray data (https://www.aging-us.com/article/203895/text, https://www.nature.com/articles/s41598-020-69330-2, among many others).

My doubt if its really ok to do that, to validate a RNAseq model in microarray data. And if so, in what ways should I normalize the microarray data?

Thanks

microarray rnaseq coxlasso fpkm
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updated by ATpoint ATpoint • written by vitor • vitor

I have the same question. Why is there no comment for this question.

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written by nuorain • nuorain

Why is there no comment for this question.

We're a community of volunteers, people answer if they have a good answer and the question is asked specific-enough. I mean, the Q here is if it is valid to validate RNA-seq with microarray, and OP presents literature which does so, so what are people supposed to say? Like, "no all literature is wrong"? Why not goping into the literature and see how they tackle it and then ask specific questions on the "how" rather than the "should I"?

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written by ATpoint ATpoint

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