I was wondering what values people typically input for the Minimum Log2 Fold Change in Limma-voom. I was told by a bioinformatician recently that the log-fold change of two or greater is considered a large fold change when looking at differential gene expression. Is this true? If not what fold change do you consider significant?
Also, does the minimum log2 fold change only impact what colour the expression values are on MD plot in galaxy? Or do different inputs affect the data generated by Limma-Voom.