browaeysrobin
commented
1 year ago Hi @aokhan
As the error messages says: "there are not enough samples per group with sufficient cells of this cell type" enough samples = 2
You cannot perform proper sample-level DE analysis (by pseudobulking+edgeR) when you don't have 2 samples or more per condition.
A workaround would be using classic cell-level based DE analyses (with wilcox / t-tests) as done in classical findMarkers functions. There is an old and maybe not functioning implementation is MultiNicheNet, however some bugs were reported #19 before. Fixing these bugs is not priority since this is not the main use case of MultiNicheNet.
Hi!
Really cool pre-print! Congratulations.
I'm trying to run your software on a data set of ours - the problem I'm running into is when I get to the DE_info analysis phase, I get the following:
_[1] "In case: Error in x[[1]]: subscript out of bounds: this likely means that there are not enough samples per group with sufficient cells of this cell type. This cell type will thus be ignored for further analyses, other cell types will still be considered." perform_muscat_de_analysis errored for celltype: HSC.MPP Here's the original error message: subscript out of bounds <subscriptOutOfBoundsError in x[[1]]: subscript out of bounds> perform_muscat_deanalysis errored for celltype: HSC.MPP
This happens for all my cell types. By and large, I get enough cells/condition before cut off (with the exception of some clusters unique to a couple of the conditions). I thought the problem might be that I only have a single sample per group? I've pasted the cell type abundance/sample graph in case helpful.
Thanks for your time - apologies if being particularly daft!