Anyone knows a way to conduct anova test on gene expression data other than the DESeq2 and Limma package?
Is there any reason why you don't want to use the Bioconductor packages designed to do this?
Actually I already did the first statistical filtering based on DESeq2 function, I want to do further analysis on the filtered genes but by Anova test on data normalized by DESeq2 on different conditions.
Sure. You could just use lm from the base package.