Papers that exclude markers from viSNE analysis
Hi all,
I'm trying to figure out how to respond to a reviewer. The question is about why I stained with 36 markers but am only using 26 markers for the viSNE analysis. I've been doing CyTOF for a long time and to me, this is very normal and there are various reasons to do this. I have explained that markers were excluded because they were used for pre-gating, are negative or very low, or are activation markers and the point of this viSNE was phenotyping (activation state to be assessed later on).
I'd really like to be able to point to CyTOF publications (other than my own) that make note of leaving markers out of the analysis or that specifically discuss the practice. Diggins, Ferrell et al. 2015 discusses leaving out negative markers from the analysis but doesn't show any data. Many papers don't specify which markers were used in viSNE, SPADE, CITRUS, etc. The original viSNE paper (El-ad et al. 2013) excludes markers but only to show that viSNE still works and not because the viSNE map will be better without these markers.
Any suggestions for papers that might help would be much appreciated!
Thanks!
Cara
I'm trying to figure out how to respond to a reviewer. The question is about why I stained with 36 markers but am only using 26 markers for the viSNE analysis. I've been doing CyTOF for a long time and to me, this is very normal and there are various reasons to do this. I have explained that markers were excluded because they were used for pre-gating, are negative or very low, or are activation markers and the point of this viSNE was phenotyping (activation state to be assessed later on).
I'd really like to be able to point to CyTOF publications (other than my own) that make note of leaving markers out of the analysis or that specifically discuss the practice. Diggins, Ferrell et al. 2015 discusses leaving out negative markers from the analysis but doesn't show any data. Many papers don't specify which markers were used in viSNE, SPADE, CITRUS, etc. The original viSNE paper (El-ad et al. 2013) excludes markers but only to show that viSNE still works and not because the viSNE map will be better without these markers.
Any suggestions for papers that might help would be much appreciated!
Thanks!
Cara