My goal is to compare transcriptome between different condition. For example, I KD gene A, gene B, genes C. And I want to know whether the consequence of KD gene A is more close to gene B or gene C. The first way I adopted is to compare CPM of KD gene A Control, KD gene A, KD gene B Control, KD gene B .... But the result is KD gene A Control and KD gene A is more close. So I think I should consider the effect of the background. I next compared the log2foldchange from DESeq2 result. But I lose the p-value information. So, what is the best way to compare the transcriptome of RNA-seq?