Hi,

I'm new at bioinformatics and use DESeq2 for the first time. I'm analyzing a RNA-seq data - 3 WT replicate and 3 mutant replicates. The MA plot show diagonal lines and I'm not sure if it's normal, or what it means. It looks too nit to me.

any ideas?

picture in the link

https://www.scribd.com/document/394171998/MAplot-DESeq2-Res

thanks in advance !

Those lines represent ratios of integers, e.g. 2/1, 3/1, 3/2, etc.

You can shrink these lines using lfcShrink() which provides reliable posterior estimates of LFC. See vignette.