const-ae / const-ae/lemur

collinearity error with control vs treatment test for multiple subjects

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Description

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

Contributor guide

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Research direction

Start with the reported handle_design_parameter error and the example formula using subject and condition. Reproduce the model-matrix rank failure with a multi-subject control/treatment design, then determine whether the supported design or its guidance needs clarification. Done means the expected two-condition analysis can be run or the limitation is clearly documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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