I downloaded expression (microarray), clinical and mutation data associated with METABRIC breast cancer study from cBIOPORTAL and I'm planning to analyze the dataset for DEGs among three subsets of individuals, subsetted based on a mutational status. I'm not familiar with using median and z-score expression values for downstream analysis. I was initially planning to set up a SummarizedExperiment object and use DESeq2 to analyze the data. Since these expression values are already normalized, I believe can't go down that path. Can I just run ANOVA (Kruskal-Wallis test) on expression values for each gene from three samples/subsets?
Any help on understanding what these median and z-score expression files exactly are, and how I may proceed with the analysis is much appreciated.