I am interested in developing a prognostic classifier in the following way:
- Use a large RNA-Seq cohort with SVM and LOOCV with RFE to develop a prognostic classifier that is able to distinguish between two phenotypes.
- I want take this classifier and test it on a different Microarray cohort to see how well these genes can discriminate between the same two phenotypes as described within the RNAseq data.
Since the distributions of these two data-types vary, we simply variance stabilize transform the counts which makes it more normal instead of neg. binomial.
The first point above is straightforward. My question is within the second point above. How can one take a classifier that was already independently created and validated to distinguish between two phenotypes using one cohort (RNAseq) but then test the accuracy of that multi-gene classifier to distinguish between the same two phenotypes using another cohort (microarray)?