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stemangiola / tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse
https://stemangiola.github.io/tidybulk/
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limma:MakeContrasts integration issues #309

Closed aodainic7 closed 7 months ago

aodainic7 commented 7 months ago

Hello Stefano, in the pipeline you can use contrasts for the test_differentialabundance() to extract the comparison you are interested in. When using a formula with interaction (e.g. treatment*genotype), you create columns with colon (treatment:genotype) and limma::MakeContrasts does not accept it. If you manually modify the design matrix by exchanging : with the function works. Cheers, Alex

stemangiola commented 7 months ago

@aodainic7 test the branch #311

aodainic7 commented 7 months ago

fixed