muscat with no replicates?
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Hi there,
I am trying to run muscat with a scRNASeq experiment but we have only one sample (replicate), 7 celltypes and 2 conditions.
I'm wondering if muscat (or any pseudobulk package) is the tool indicated for this analysis or if I would have to try with SCDE or MAST.
Could you help me?
Many thanks!
I'd recommend having a look at section 2.12 of the edgeR user guide. Here's part of what it says. Lots of other comments/thoughts/suggestions given online if you search for, e.g., "DGE without replicates".
"edgeR is primarily intended for use with data including biological replication. Nevertheless,
[...] it sometimes happens that only
one library can be created for each treatment condition. In these cases there are no replicate
libraries from which to estimate biological variability. In this situation, the data analyst is
faced with the following choices, none of which are ideal. We do not recommend any of
these choices as a satisfactory alternative for biological replication."