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saeyslab / muscatWrapper

Easy muscat differential expression analysis and visualization
GNU General Public License v3.0
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Can't perform multifactorial design and complex contrast #3

Closed zlin-bioinfo closed 11 months ago

zlin-bioinfo commented 11 months ago

Hi, Thank you for developing the practical package to facilitate pseudobulk DE analysis.

Though it was not exemplified, I tried to perform a multifactorial design and complex contrast like the MultiNicheNet vignettes (https://github.com/saeyslab/multinichenetr/blob/main/vignettes/multifactorial_analysis_BreastCancer.md). The muscat_analysis() doesn't accept contrasts_oi = c("'(OnE-PreE)-(OnNE-PreNE)','(OnNE-PreNE)-(OnE-PreE)'"), and showed Error in muscat_analysis(sce = sce, celltype_id = celltype_id, sample_id = sample_id, : conditions written in contrasts_oi should be in the condition-indicating column! This is not the case, which can lead to errors downstream.

BTW, the get_abundance_info() doesn't accept multiple covariates when I specified a vector of characters.

Would appreciate any suggestions regarding the issues. Thanks!