These are chat archives for nickschurch/Kallisto_Salmon_Sailfish_comparison
ok, so the next figure compares the output from two tools (I'll start with Sailfish and Salmon) for each condition for each annotation.
The axes are log10 of the mean TPM of a transcript across the replicates of a given condition in a given annotation for each tool. The red dotted line is the 1:1 relation. The plot is actually a plot of point density (to avoid plotting zillions of points) and the colour represents the log10 of the number of points in the 'hex'. This range is from 1 point in a hex (purple) to thousands (red).
The dark grey lines on the background are the 1standard deviation error bars for all the points. For most points this is small but for some (particularly low TPM) transcripts it is larger and can be asymetric. It gives us some kind of idea about the level variation in the measurements The Pearsons correlation (and 95% confidence intervals) are shown in the upper left corner.