Download expression matrix with cell cluster information indicated in cell IDs


Appreciations for Cellenics platform for single cell analysis. After cell clustering and annotation, I would like to do a deconvolution analysis for bulk RNA data to infer cell type proportions. For doing so, I need a single cell expression matrix as a reference. The current Cellenics can export an expression matrix. However, the output matrix does not indicate any metadata information in the cell ID. It’s something like “GGGACCTGTCATTGCA-1_3”, which from my understanding should be the sequencing index of the cell. What would be more useful for a cell ID I think, may be something like “Cluster1_sample2.cell3”. Will it be possible to download expression matrix with metadata indicated? Also, what normalisation method has been applied to the matrix data? The deconvolution method I am trying to use recommend the sc data not to be log transformed. I am wondering if more options can be added to the feature of the output expression matrix.

More specifically, I am using the “AutoGeneS” package to do deconvolution. The required input of the single cell data reference is an expression matrix featuring different cell types. Each row of the matrix file is a gene. The whole matrix contains about 4000 highly variable genes. Each column of the matrix is a cell type. Each value in the matrix is the normalised mean expression count of a cell type for each gene.

Thanks for any advices!

Best wishes,