Thanks for providing this interesting tool. Cool you explain more in-depth how to generate reference profiles? In the vignette you state that it
"... consists of a gene (rows) by cell type (columns) matrix containing transcript-per-million (TPM) gene expression values normalized for total mRNA abundance."
Further down, you write that
"Reference profiles for deconvolution are usually generated by differential expression analysis on bulk RNA-seq generated from isolated cell types or cell-type clusters identified by single cell RNA-seq."
What measure would you want me to use from DE analysis on scRNA-seq clusters as reference? Also, is this DE analysis a comparison between clusters or between conditions? And how would you normalize for total mRNA abundance from scRNA-seq data?
Optimally, some examples for creating reference profiles would make it really easy for people to start using your tool.
rrydbirk
commented
1 year ago
Thanks for providing this interesting tool. Cool you explain more in-depth how to generate reference profiles? In the vignette you state that it
"... consists of a gene (rows) by cell type (columns) matrix containing transcript-per-million (TPM) gene expression values normalized for total mRNA abundance."Further down, you write that
"Reference profiles for deconvolution are usually generated by differential expression analysis on bulk RNA-seq generated from isolated cell types or cell-type clusters identified by single cell RNA-seq."What measure would you want me to use from DE analysis on scRNA-seq clusters as reference? Also, is this DE analysis a comparison between clusters or between conditions? And how would you normalize for total mRNA abundance from scRNA-seq data?
Optimally, some examples for creating reference profiles would make it really easy for people to start using your tool.
BR
Rasmus