5 months ago by
Palo Alto, CA, USA
thank you all for your suggestions ! if I may ask for another suggestion please regarding scRNA-seq analysis:
shall we have 2 scRNA-seq samples that do not align too well by using either CCA (in Seurat 2) or Seurat 3 methods (with batch correction in Harmony, Liger, Conos, etc, as we have discussed above), the functions that compute the CONSERVED MARKERS (FindConservedMarkers) or DIFFERENTIAL MARKERS (FindMarkers) likely fail on the cell clusters that DO NOT ALIGN.
how could I still compute the CONSERVED or DIFFERENTIAL MARKERS on the cell clusters that DO align (in some extent) ? If anyone has the experience and would like to share it please. Many thanks for your suggestions; be safe, stay healthy,
ps : 've posted a similar question on Seurat github web page, and i have not heard from Seurat's authors about it for a while.