DEGs analysis of RNA-seq multiple conditions

Question

[Little.G]

I would like to compare RNA-seq data from 4 different cells of my plant. I did all the upstream processes, then i'm doing the statistic analysis of DEGs now. I only have a script using edgeR for pairwise analysis. But i would like to do statistic test with all my data at once (in my idea >> ANOVA and followed by multiple comparison test like Duncan). Do you have a script to complete this? Or do you have another way to do this by other programs?

Please give me some suggestion Thank you in advance :)

Answer 1

[russhh]

You can do LRT tests in edgeR using glmLRT. Once you've done this across all your contrasts you can do nested analysis of the individual contrasts on the all-contrast hits

[Kevin Blighe]

Indeed, as per russhh. Please take a read of:

• EdgeR user guide
• DESeq2 Vignette