I have been dealing with expression data for about 4 years (both microarray and rna-seq). but this question still confuses me when I do data preprocessing. 1) My opinion is that at least we should do low expressed gene filtration first. Reason is that: the aim for quantile/log2 transform is to make the data distribution more proper. but if quantile/log2 goes first and then followed by low-expressed gene filtration, we may break the distribution.
2) For log2 transform and quantile normalization, I really don;t know which one goes first.
Thank you in advance for your time and valuable suggestion.