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HelenaLC / muscat

Multi-sample multi-group scRNA-seq analysis tools
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pbDS(pb, design = mm, contrast = contrast) error #136

Open Jadeapple opened 3 months ago

Jadeapple commented 3 months ago

I ran pbDS(pb, design = mm, contrast = contrast) and got the following error: Error in pbDS(pb, design = mm, contrast = contrast) : Specified filtering options result in no genes in any clusters being tested. To force testing, consider modifying arguments 'min_cells' and/or 'filter'. See '?pbDS' for details.

then I ran pbDS(pb, design = mm, contrast = contrast,min_cells=1,filter="none"), and the same error appeared. what should I do?

HelenaLC commented 3 months ago

Independent of filter=..., the function will drop samples with fewer than min_cells in a the cluster being tested. Then, the rank of the design matrix is checked and at least two samples need to be present per group. So... my intuition is that your clusters aren't represented by at least two replicates in both groups. Maybe you could screenshot & post something like table(sce$sample_id, sce$group_id) and table(sce$sample_id, sce$cluster_id) to better understand what's causing the issue?

Jadeapple commented 3 months ago

Independent of filter=..., the function will drop samples with fewer than min_cells in a the cluster being tested. Then, the rank of the design matrix is checked and at least two samples need to be present per group. So... my intuition is that your clusters aren't represented by at least two replicates in both groups. Maybe you could screenshot & post something like table(sce$sample_id, sce$group_id) and table(sce$sample_id, sce$cluster_id) to better understand what's causing the issue?

you are right，I have no replicates, only one sample per group. So I can't use this method to do differential analysis?