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Consider replacing
dea_limma/workflow/scripts/limma.R
Lines 99 to 103 in 175762a
| # check if the model represented by the design matrix has full rank ie linearly independent columns, which is required to make the model identifiable! | |
| # new: more efficient and computationally stable compared to the svd() function, especially for large matrices, and it does not require rounding the singular values or checking for non-zero values. | |
| if(qr(model_matrix)$rank != ncol(model_matrix)){ | |
| stop("Error: The design matrix representing your model does not have full rank, rendering the model not identifiable.") | |
| } |
with limma's function nonEstimable, which shows problematic coloumns and is.fullrank as TRUE/FALSE check.
https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/is.fullrank
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