I used HISAT2 and StringTie2 to analyze RNA-seq , and finally obtained the FPKM for per gene. Then I made a boxplot for gene expression in all samples. Unfortunately, I found that the mediate value across samples was not identical, so do I need to do quantile normalization for FPKM. I also checked this post (Rnaseq Fpkm Quantile Normalization) and found that it was not necessary to do quantile normalization. Thanks in advance, best,
FPKM is not recommended for any kind of differential analysis between samples. Get the raw counts after aggregating to the gene level (e.g. using tximport) and then normalize with proper approaches such as
DESeq2. The vignettes and papers cover the topic of normalization for various purposes.
DESeq2 are other popular choices depending on the application. For information why FPKM is not recommended, please use google and the search function and see benchmarking papers comparison normalization methods.