As you know, there are some Bioconductor packages like limma, which were first introduced for microarray data but then after the emergence of RNA-seq technology, those packages can be also used for new technology by some transformations like "voom" in limma. I wanted to ask, in your opinion, what normalization or preprocessing step is needed for this kinds of packages. Or can you send me any links/papers regarding this subject. Right now I am using "voom" for this purpose but then I received negative values for the expression of the counts as it calculates the log of the transformation and I think "voom" transformation is not an optimum way for my method.
Thank you in advance