| PMC full text: | Published online 2018 Apr 17. doi: 10.1038/sdata.2018.61
|
Figure 2
Effect of uniform processing and batch effect removal on gene expression levels in GTEx and TCGA.
Two-dimensional plots are shown of principal components calculated by performing PCA of the gene expression values of bladder, prostate, and thyroid samples from GTEx and TCGA. (a) PCA of the level 3 data, i.e., the expression data from GTEx and TCGA. GTEx expression data was quantile normalized (see Supplementary Fig. S1B). (b) PCA of the expression data after uniform processing through our pipeline, before batch bias correction. (c) PCA of the expression data after uniform processing through our pipeline, after batch bias correction.
