concatenatings samples from different runs-viSNE
Hi,
Pretty new with Cytof analysis...
I'm trying to concatenate samples from 2 different cytof experiments (same staining panel and protocol, experiments done on different days) for viSNE analysis. Unfortunately, I don't have the same technical control ran in both experiments but what I notice is that the visne plots of all samples ran in experiment 1 have the same basic structure, i.e., same populations on the same islands but all samples ran in experiment 2 show these populations on a different island. I wonder why do I get different visne structure for 2 different experiments even when they are analyzed together in the same visne analysis run. Does anyone else have this issue too?
Thanks!
M
Pretty new with Cytof analysis...
I'm trying to concatenate samples from 2 different cytof experiments (same staining panel and protocol, experiments done on different days) for viSNE analysis. Unfortunately, I don't have the same technical control ran in both experiments but what I notice is that the visne plots of all samples ran in experiment 1 have the same basic structure, i.e., same populations on the same islands but all samples ran in experiment 2 show these populations on a different island. I wonder why do I get different visne structure for 2 different experiments even when they are analyzed together in the same visne analysis run. Does anyone else have this issue too?
Thanks!
M