I read this post and was still confused about how to use the scale feature of the heatmap command: Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
For example, the following source states that
scale=None is the default standard of use in the
heatmap.2 command (see comments section of this link): https://biomickwatson.wordpress.com/2015/04/05/you-probably-dont-understand-heatmaps/
However, I am still confused when and why to use the scale option. Is using the default
scale=None option the safer (more general) alternative when creating heatmaps? For example, would you only really care to scale by row if you have a time-course RNA-seq experiment?
I would be very grateful if someone could shine some light on using the scale option in the heatmap and heatmap.2 commands.