Hello!

I am working on differential gene expression of cell free RNA. In this process I have created the count matrix then calculated the log of count per matrix then calculated the Z_score and calculated the variance using log and created these boxplots. So these 2 boxplots are of 2 different datasets. Is it good to go for further differential gene analysis?

If you have and RNA-Seq count matrix, use dedicated tools for DE analysis e.g. DESeq2, edgeR or limma .There are specifically designed for such analysis, other standard statistics test such as t-test are under-powered.

i have used DESeq2 but same issue. if u have a reference for these please share.