Hello,
I recently read your DISSECT paper and had a question about how you ran MuSiC on the real PBMC8k dataset to generate Figure 2.
As far as I understand, MuSiC requires multiple subjects in the single-cell reference data. However, the PBMC8k dataset appears to contain cells from only one donor. I tried running MuSiC using the code from your repository:
> colnames(df_celltypes) <- c("cellType", "SubjectName")
> df_celltypes$cellTypeID <- df_celltypes$cellType
> df_celltypes$subjectID <- df_celltypes$SubjectName
> rownames(df_celltypes) <- colnames(df)
>
> pheno_data <- AnnotatedDataFrame(data = df_celltypes)
> eset <- ExpressionSet(as.matrix(df), phenoData = pheno_data)
>
> est.prop <- music_prop(
> bulk.eset = eset_bulk,
> sc.eset = eset,
> clusters = "cellType",
> select.ct = unique(df_celltypes$cellType),
> verbose = FALSE
> )
In the repository code, all cells seem to be assigned to "donor1". When I try this, MuSiC crashes because the reference contains only a single donor.
Could you explain how you performed the MuSiC analysis for this dataset? I may be missing something, but I would like to understand how the single-donor issue was handled.
Best regards,
Sergej Ruff
Hello,
I recently read your DISSECT paper and had a question about how you ran MuSiC on the real PBMC8k dataset to generate Figure 2.
As far as I understand, MuSiC requires multiple subjects in the single-cell reference data. However, the PBMC8k dataset appears to contain cells from only one donor. I tried running MuSiC using the code from your repository:
In the repository code, all cells seem to be assigned to "donor1". When I try this, MuSiC crashes because the reference contains only a single donor.
Could you explain how you performed the MuSiC analysis for this dataset? I may be missing something, but I would like to understand how the single-donor issue was handled.
Best regards,
Sergej Ruff