Update FAQs.md

FAQs.md

@@ -23,11 +23,29 @@ Final note: Insitutype splits big clusters with higher counts more aggressively
 
 ### Updating reference profiles
 
+Cell typing's biggest challenge is using a reference dataset from a different platform. Platform effects between single cell and spatial platforms can be profound. 
+Insitutype has 3 treatments for reference profiles:
+1. Use as-is
+2. Choose anchor cells, then rescale genes based on estimated platform effects. (Less aggressive, only fits gene-level effects.)
+3. Choose anchor cells, then refit the reference profiles entirely. (Most aggressive, fits a new value for every gene x cell type.)
+
+
+![image](https://github.com/Nanostring-Biostats/InSituType/assets/4357938/e58f8196-f226-4641-8dfa-bafd9b3dbfae)
+
 
 ### Targeted subclustering
 
 
-### Choosing nclust
+### Which genes to use
+
+Insitutype was designed using 1000-plex CosMx data, where we found it most powerful to use all genes in the panel. 
+In our new 6000-plex data, it's worth considering using Insitutype on a well-chosen subset of genes. As a rule of thumb, genes should be retained if either of the following applies: 
+1. They have solidly above-background expression in the CosMx data
+2. They have moderate-to-high expression in at least one reference profile
+
+For typical 6000plex experiments, we speculate that cell typing using somewhere between 3000-5000 genes would be optimal. 
+
+
 ### Choosing nclust