Does anyone have the solution to this error message?
I am working with Kallisto and Sleuth to analyze some RNA seq data. I have a control set of macula data and a set of macula data with AMD. I am trying to analyze differential gene expression between the two sets.
Design table: sample Tissue Condition AMD_macula.11 Macula AMD AMD_macula.12 Macula AMD AMD_macula.14 Macula AMD AMD_macula.17 Macula AMD AMD_macula.18 Macula AMD AMD_macula.19 Macula AMD ctrl_macula.10 Macula nodisease ctrl_macula.13 Macula nodisease ctrl_macula.15 Macula nodisease ctrl_macula.16 Macula nodisease ctrl_macula.4 Macula nodisease ctrl_macula.6 Macula nodisease
I have created my sleuth object and now I am trying to fit the models so I can run linear regression and wald tests.
so <- sleuth_fit(so, ~sample + Condition,'full') so <- sleuth_fit(so, ~Tissue, 'Tissue') models(so)
When running these, I cannot get past creating the first model because I am getting this error that is saying that the system is computationally singular.
> so <- sleuth_fit(so, ~sample + Condition,'full') Error in solve.default(t(X) %*% X) : system is computationally singular: reciprocal condition number = 3.82836e-18
Does anyone know how to solve this? I believe something is wrong with my design table, but I cannot think of how to fix it.