New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Fig 3
DEA analyses of TCGA-BRCA data comparing luminal subtypes with normal samples.
A-B) Volcano plots are shown where only those genes with logFC higher than 6 or lower than -6 are labelled and only the significant up- or down-regulated genes are shown as dots. We carried out DEA using the limma (A) or edgeR pipelines (B) of TCGAbiolinks. C) The correlation plot between the logFC estimated by the two pipelines for the top 500 DE genes is shown. The genes discussed in the main text are highlighted in bold. D) The intersect between all the DE genes estimated by the two pipelines is shown using UpSet.