I am trying to analyse the trajectories of a dataset with a binary condition and two lineages (as per the slingshot analysis).
When I apply tradeSeq to obtain the signifficative genes should I use the genes from "ConditionTest" or the ones from "AssociationTest" from their package? Given that I already have the conditions on separate lineages it seems logical to examine each lineage separately and find the genes contributing to each one. The other option is to use "ConditionTest", but would it pick one of the four lineages as a reference to do the test or would it group the two lineages 1 (one for each condition) and the two lineages 2?
Thanks for developing this tool, is proving really interesting in my analyses. Also, thanks in advance for answering my doubts.
Hi,
I am trying to analyse the trajectories of a dataset with a binary condition and two lineages (as per the slingshot analysis).
When I apply tradeSeq to obtain the signifficative genes should I use the genes from "ConditionTest" or the ones from "AssociationTest" from their package? Given that I already have the conditions on separate lineages it seems logical to examine each lineage separately and find the genes contributing to each one. The other option is to use "ConditionTest", but would it pick one of the four lineages as a reference to do the test or would it group the two lineages 1 (one for each condition) and the two lineages 2?
Thanks for developing this tool, is proving really interesting in my analyses. Also, thanks in advance for answering my doubts.
Best, Jaime