2.9 years ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
No, there is no requirement for equal sample sizes. If you can run edgeR for differential expression, then you can also call calcNormFactors() to do TMM normalization. There is no additional requirement.
To be honest, I can't really figure out what your concern is. It isn't meaningful to say that the number of DE genes is different in each sample -- that is actually impossible, because the number of DE genes is a characteristic of the whole experiment, not something that varies from sample to sample.
Perhaps you are worried that the number of DE genes must be somehow balanced in each direction, equal up and down. That also is not necessary.