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xuranw / MuSiC

Multi-subject Single Cell Deconvolution
https://github.com/xuranw/MuSiC
GNU General Public License v3.0
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Music input file #132

Open mgp2022 opened 3 months ago

mgp2022 commented 3 months ago

I have snRNA-seq dataset from literature called sc in S4 Seurat.

I converted it to SingleCellExperiment using this function: sc.sce <- as.SingleCellExperiment(sc)

However, in the sc.sce object something is strange. Instead of counts, I see logcounts when I look under assays->data->listData-> logcounts

logcounts is a S4 [2000x220170] (Matrix::dgCMatrix)

When I run MuSiC is gave me an error that function cannot find the right slot, thus we converted logcount name to count, which I am pretty sure is incorrect.

Could you advise what is the correct approach in this case? I worry that I am using log counts into MuSiC and that may affect the results.

I cannot use MuSiC2 as it is not supported by our work Custer environment.

gongzhongyan commented 3 months ago

I am also confused with the input file for running MuSiC. I have an annotated Seurat object and I went through sc.sce <- as.SingleCellExperiment(seurat.object) and somehow the dataformat converted has not been compatible with the MuSiC algorithm. I wonder if you have a detailed step-by-step tutorial of how to construct the write SingleCellExperiment object preferably if from Seurat object so that can help running MuSiC smoothly?

mgp2022 commented 3 months ago

I think I solved it. You have to specify the assay, in this case RNA, as written below:

as.SingleCellExperiment(your_Seurat_object, assay = "RNA")

When I left assay as either: 1) default: as.SingleCellExperiment(your_Seurat_object) OR 2) specify assay as NULL as.SingleCellExperiment(your_Seurat_object, assay = NULL)

That gave me logcounts and no counts. The whole input was wrong and gave errors.

This made Music fail every time as it could not find the slot for "counts".

At first, I forced the name change from logcounts to counts and that worked for Music, but I think the input to Music function should not be logcounts but counts, based on their documentation.

When you specify the assay = "RNA", SingleCellExpriment will add the right assay to the sc file you are creating. Hopefully, that will fix it for you as well. This was very frustrating.