Figure 3
From: Modeling non-uniformity in short-read rates in RNA-Seq data
Fitting counts for the Apoe gene. Black vertical lines represent counts (experimental values or fitted values) along the Apoe gene (with the UTR and a further 100 nucleotides truncated). (a) Counts of reads (true values) in the Wold brain data. This is the same as the central part (black vertical lines) of Figure 1a. (b) Counts of fitted reads using the Poisson linear model. We use the other 99 genes of the top 100 genes to train the linear model, which is then used to predict the counts for Apoe. This prediction has a (cross-validation) R2 = 0.54. (c) Counts of fitted reads using MART. We use the other 99 genes of the top 100 genes to train MART, which is then used to predict the counts for Apoe. This prediction has a (cross-validation) R2 = 0.69.