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collinearity error with control vs treatment test for multiple subjects #9
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Hi shobhit, thank you :) To fit a multi-subject two-condition analysis, set the design to If you notice that the subject effects are so strong that corresponding cells from different subjects are not aligned after calling Best, |
Dear Constantin, thank you once again |
Yes. The way the replicates are specified is through the |
thanks once again! I will give it a try and get back to you. |
Hi,
Really interesting work and really thankful for the general ease of use!
The data I have has several subjects,each belonging to either control or treatment so the formula i am trying is
lemur(sce, design = ~ subject + condition, n_embedding = 30, test_fraction = 0.5)
however I am getting this error
Error in handle_design_parameter(design, data, col_data) :
The model matrix seems degenerate ('matrix_rank(design_matrix) < ncol(design_matrix)'). Some columns are perfectly collinear. Did you maybe include the same coefficient twice?
Now my understanding is that the one-hot encoding for each of control and treatment is being declared as collinear, could you please tell me how one can run a typical multi-subject (assuming them to be biological replicates) two condition analysis ..
appreciate any help.
thanking you
shobhit
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