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saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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How to proceed when a cell type does not have enough number of cells in a group #31

Closed anemartinezlarrinaga2898 closed 11 months ago

anemartinezlarrinaga2898 commented 11 months ago

Hello!

Im running multinitchenet in a single cell object where I have three groups in different cell types. However when I run the

DE_info <- get_DE_info(sce = sce, sample_id = sample_id, group_id = group_id, celltype_id = celltype_id, batches = batches, covariates = covariates, contrasts_oi = contrasts_oi, min_cells = min_cells, findMarkers = TRUE)

I get the following error: ""excluded cell types are:"

How should I proceed? Should this cell types be removed? What is the community doing or the library guys doing?

browaeysrobin commented 11 months ago

Hi @anemartinezlarrinaga2898

the "excluded cell types are:" message is a warning message, not an error message. You can just continue the analysis.

Note that we advise against using findMarkers = TRUE. This option is more included for internal testing/comparisons and not for use by end users.