about correcting the batch effects in LIMMA and SVA, 'd appreciate having your comments :
assuming that we have a set of RNA-seq data (no treatment, + treatment) in many distinct BATCHES, would the linear model in LIMMA :
design <- model.matrix(~0 + BATCH + Treatment, data=RNA)
suffice to correct for batch effects, or shall we additionally use COMBAT (as it is described in the SVA package : https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf ) in order to obtain the corrected counts ?
thanks a lot,