How do I create a Sleuth Wald Test

Question

[scottschu97]

I am currently trying to check for differential expression between samples of AMD Macula and Control Macula. I have successfully created a linear regression test but I am having trouble creating a Wald Test.

Here is my design table:

 > s2c
            sample tissue  condition
 1   AMD_macula.11 macula        AMD
 2   AMD_macula.12 macula        AMD
 3   AMD_macula.14 macula        AMD
 4   AMD_macula.17 macula        AMD
 5   AMD_macula.18 macula        AMD
 6   AMD_macula.19 macula        AMD
 7  ctrl_macula.10 macula no.disease
 8  ctrl_macula.13 macula no.disease
 9  ctrl_macula.15 macula no.disease
 10 ctrl_macula.16 macula no.disease
 11  ctrl_macula.4 macula no.disease
 12  ctrl_macula.6 macula no.disease
 13  ctrl_macula.7 macula no.disease
 14  ctrl_macula.8 macula no.disease
 15  ctrl_macula.9 macula no.disease

Here is my code for fitting the models "full" and "reduced":

 so <- sleuth_fit(so, ~condition, 'full')
 so <- sleuth_fit(so, ~1, 'reduced')

 > models(so)
 [  full  ]
 formula:  ~condition 
 coefficients:
     (Intercept)
     conditionno.disease
 [  reduced  ]
 formula:  ~1 
 coefficients:
     (Intercept)
 >

Here is my code for attempting to create a Wald Test:

 # Create a Wald Test
 sleuth_wt(so, which_beta = 'conditionno.disease', which_model = 'full')

Here is the error I am getting:

 > sleuth_wt(so, which_beta = 'conditionno.disease', which_model = 'full')
     sleuth object

 bears: 15 
 design: NULL

Any help would be greatly appreciated!

Answer 1

[Kevin Blighe]

You have not executed the following line:

so <- sleuth_prep(s2c, extra_bootstrap_summary = TRUE)

[scottschu97]

Apologies,

I have executed the line and did not include it in the post

[Kevin Blighe]

Okay, my apologies, you may have more luck posting on the GitHub page for errors with Sleuth: https://github.com/pachterlab/sleuth/issues

I have seen a couple of Sleuth errors reported on Biostars with no answers, but the reports receive answers from the program developers themselves on the GitHub page.