I have to use 2 data sets. one of them for train and another one for test. My train data set belongs to TCGA and its workflow type is FPKM-UQ (also RNA-seq by HTSeq-FPKM and HTSeq-count are available in GDC portal) but my test RNA-seq was normalized by Transcript per million (TPM) method. My problem is for getting reasonable result should I use these 2 dataset convert to unique normalized method or I can use one data set by FPKM-UQ normalization method and one data set for testing my model by Transcript per million (TPM) method?
I appreciate if anybody share his/her comment with me.