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For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.

4 votes
Accepted

What does aov(glm model) actually do in R?

It's not appropriate to run aov on a GLM model. aov assumes normally distributed data and it runs on a GLM as if it was a least squares linear model. It uses the working responses and working weights …
Gordon Smyth's user avatar
2 votes

Comparing differential expression across samples - is batch effect correction needed?

There is no need for batch correction because all your comparisons are within batch. As long as you are making comparisons for each line, and treatment and control for the same line are in the same ba …
Gordon Smyth's user avatar