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DEGs analysis of RNA-seq multiple conditions

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 :)

rna-seq rna-seq sequencing
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written by Little.G • Little.G

1 answer

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

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written by russhh russhh

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