Problem with plot_bootstrap function in sleuth

Question

[lalvarez]

Hi all,

I'm pretty new with kallisto and sleuth, but thanks to the online information I'm getting result of my RNA-seq analysis. I'm following this pipeline https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html to see different gene expresion.

Now I'm triying to run "plot_bootstrap function"

In the example of the web say:

plot_bootstrap(so, "ENST00000263734", units = "est_counts", color_by = "condition")

In my case the most expressed transcript is called TRINITY_DN3505_c0_g1_i5 and my factor is "seasons". Then I tried with that:

plot_bootstrap(so, "TRINITY_DN3505_c0_g1_i5", units = "est_counts", color_by = "season")

But I got the error:

Error in obj$bs_quants[[1]] : subscript out of bounds

Can you help me with the meaning of this error?

I was reading other post about this error, and it appears to mean that you are calling to something that doesn't exits... but I don't undersand, because in my case the name of the transcript is correct and also the name of the factor... both exist. So... I don't know.

Any suggestion could be helpful.

Answer 1

[lalvarez]

I got the answer in sleuth_prep function.

extra_bootstrap_summary: if TRUE, compute extra summary statistics for estimated counts. This is not necessary for typical analyses; it is only needed for certain plots (e.g. plot_bootstrap). Default is FALSE.

So is necessary to add extra_bootstrap_summary=T if tou want to see a plot_bootstrap. Like in my case so <- sleuth_prep(s2c, ~ , extra_bootstrap_summary=T) Then this works plot_bootstrap(so, "TRINITY_DN3505_c0_g1_i5", units = "est_counts", color_by = "season")

[Kristoffer Vitting-Seerup]

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