I am new to galaxy. I have been trying to use RUVseq to be specific remove unwanted variation tool to remove some confounding factors for my sequencing data. However, the tool only generates plots and the covariate files for each method. My question is: how do I get the normalised data or rather how do I apply correction on DESeq2. I have tried ways, but it seems that the PCA plots generated were always the same.
Can someone help me out with this? I have searched over and over but there’s no definite answer to this.