I need to remove batch effect between two RNA-seq datasets and get the corrected expression profile for downstream analysis, such as clustering. One data is from TCGA and the other is provided with only FPKM/TPM values. However，the current tools dealing with bulk RNA-seq data are count-based(ComBat_seq, svaseq and RUVseq) and other tools, such as removeBatchEffects, ComBat and sva, are designed for microarray data . Is there any way to solve my problem? And if I also have microarray data, can I remove batch effect between RNA-seq data and microarray data?
Thanks in advance