Supplementary Figure 3: Abundance vs. fold change accuracy on Polyester simulated data
From: Salmon provides fast and bias-aware quantification of transcript expression
The log2 fold change between the estimated and true abundances as a function of the true abundance (measured in TPM), for all methods and for all replicates of both simulated “conditions” (each row displays points from all samples within a given condition). The top row corresponds to the 8 samples simulated from the data showing the weak fragment GC content bias, while the bottom row corresponds to the 8 samples simulated from the data showing the stronger fragment GC content bias. Points with an estimated log2 fold change of > 0.5 or < -0.5 are colored red. The fraction of red points appears in the upper right-hand corner of each plot. Salmon consistently demonstrates log fold changes closer to 0 than either kallisto or eXpress, across most of the range of expression.
