I would like to use the WHOLE CORTEX & HIPPOCAMPUS - 10X GENOMICS (2020)
WITH 10X-SMART-SEQ TAXONOMY (2021) mouse data to study the expression of specific genes in the cell clusters as defined by Allen. I have a few questions though.
- In the median and in the trimmed means expression datasets, do 0s mean no expression of that gene in that specific cluster?
- Is it best to use the median or trimmed means expression to determine expression Vs no expression of a gene in a cluster? On the transcriptomic explorer trimmed expression is used so should I consider that more appropriate?
- I understand that with trimmed means I will be able to see expression without any extreme values but in that case, would I have to use a cut-off value to determine expression? I figure it’s more straightforward with medians as there are no values very close to 0, which is often the case with trimmed means.
Any suggestions would be greatly appreciated.