Hello

I am trying to do some statistical analysis on RNA-Seq data. I have 5 different treatments with biological duplicates for each conditions. I am trying to analyze these data for differential gene expression among different treatments. Since pairwise testing of the data in initial stages would lead to greater amount of false discovery in genes, what is the best approach to do statistical analysis on multiple groups? Would performing ANOVA analysis be a good method to start with? And what bioinformatics package could I use to perform this analysis (edgeR or BaySeq)?

Thanks
EdgeR would work for you (it's not the only one, but it's one I've used successfully for these types of experiments). It can handle more complex experimental designs in a better way than just doing a large collection of pairwise tests.

In the <a href="http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf">manual</a>, check out the sections "More complex experiments (GLM functionality)" and "An ANOVA-like test for any differences". In the GLM mode, you can give it an arbitrary experimental design with multiple treatments, replicates, and batches, and it will do the "right thing".