DeepTools plotProfile y axis units?

Question

[mcsimenc]

Hi,

Does anyone know what the units are of the y-axis in profile plots made by plotProfile and plotHeatmap?

Say I used bamCompare to create a bigwig with units of log2 fold change, computeMatrix to make a matrix file, and then plotProfile or plotHeatmap. Is the y-axis of the profile plot the mean log2 fold change? median log2 fold change? It seems to be an average of each position across all features in that cluster.

Thanks!

Matt

Answer 1

[Devon Ryan]

The units are whatever is in the bigWig files. If you used the default mean summarization in the profile with a bigWig file made with bamCompare (default log2 ratio) then the Y axis is "mean normalized log2 ratio between sample X and sample Y" or something along those lines.