After sleuth fit, I found that there is one treatIgG4 lost, which can not be used in which_beta. Following the walkthrough, while treatControl can be choosed in which_beta ; so is the heatmap can be used to show the differential expression among the treatments?
If I change the which_beta to treatIgG1.. treatIgG4, I would get four different heatmaps, then which one to use, and how to interpret the heatmap?
Thank you very much!
so <- sleuth_fit(so, ~treat, 'full') ## expect to compare Control, IgG1, IgG2, IgG3, IgG4,
so <- sleuth_fit(so, ~1, 'reduced')
so <- sleuth_lrt(so, 'reduced', 'full')
oe <- sleuth_wt(so, which_beta='treatIG1')