I am interesting in clustering my single cell data to identify clusters and then figure out if certain genes differ in expression profiles and then try to link them to developmental stages.
1. So, to be able to compare gene to gene expression, I suppose the expression scores should be corrected for gene length. Does SC3 do this somehow? I don't pass in a gene length argument at any point, so I was wondering about this.
2. I am using salmon count data (using tximport) for SC3. Now I was wondering if I could use salmon 'length scaled tpm' for SC3 clustering. Does it make sense to use this? If yes, how would I go about doing that?