Question: How do I create a Sleuth Wald Test
gravatar for scottschu97
12 months ago by
scottschu9710 wrote:

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 
 [  reduced  ]
 formula:  ~1 

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!

rna-seq bioconductor sleuth R • 847 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe37k • written 12 months ago by scottschu9710
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

You have not executed the following line:

so <- sleuth_prep(s2c, extra_bootstrap_summary = TRUE)
ADD COMMENTlink written 12 months ago by Kevin Blighe37k


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

ADD REPLYlink written 12 months ago by scottschu9710

Okay, my apologies, you may have more luck posting on the GitHub page for errors with Sleuth:

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.

ADD REPLYlink written 12 months ago by Kevin Blighe37k
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