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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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Is it possible to compare more than 2 groups of samples #114

Closed qicaibiology closed 4 years ago

qicaibiology commented 4 years ago

Hi: Thanks for developing this tools and the generous help on using this tool. I have a question on if it is possible to compare more than 2 groups of samples: eg, I have 4 stages of samples, each has 2 replicates. So far, I have compared each 2 combinations and merge the tables together. I am wondering if it is possible to feed all of them to the software at once and got a master table to filter?

Thank you very much?

Cai

dg520 commented 4 years ago

Hi @qicaibiology , The short answer is: no, there is no module in IRFinder that is able to directly achieve what you want. But you can use the GLM-based approach to create all comparisons from all combinations and merge those tables manually. IRFinder's GLM uses DESeq2 kernel. You can consult DESeq2 manual to see how to do this.

Best, Dadi

qicaibiology commented 4 years ago

Thank you for letting me know this.