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!