delta-CN and delta-RNA

[gianasco]

Hi @kieranrcampbell,

I have a question possibly related to issue 13#issue, concerning model fits and outputs interpretation. From the output of plot_clonealign (version 2.0), I see that the delta of the scaled lognormalized RNA expressions among two clones do not proportionally reflect the CN delta. For example, considering one chromosome, when the CN is 3 and CN delta between two clones is zero, I do not find a zero delta between the RNA z-scores for expressions corresponding to the same two clones. This happen also the other way round, if there is a variation in CN-space, I do not necessarily see an approximate proportional variation on the corresponding RNA expression. What I mostly can appreciate is that the sign of the delta between DNA and RNA are consistent.
It seems a similar behaviour is also present in the plots of the main paper, so I guess it's alright and I just wanted to check. Is there any clonealign function plot to add RNA counts to the above plots?

[kieranrcampbell]

Hi @gianasco

Do you have an example plot so I can get a better idea of what you mean?

Thanks

Kieran