I have obtained TCGA RNAseq - IlluminaHiSeq data from UCSC Xena. They have downloaded Level_3 data from TCGA DCC (file names: *.rsem.genes.normalized_results) and log2(x+1) transformed.
I want to find differentially expressed genes for particular cancer, say, for LIHC using primary solid tumour and solid tissue normal samples using the data obtained from there.
I know that packages like DESeq2 and EdgeR are widely used to find differentially expressed genes for RNASeq data. But they require raw counts data. I have also used R packages like limma and SAM to find differentially expressed genes from DNA Microarray data.
But I don't know which packages or methods are good to find differentially expressed genes from RNASeq rsem and log2(x+1) transformed data as I have collected above.
If anyone can help me out.
Thanks in advance.