How do I get statistics for the interaction effect in my RNA-Seq?
Hello All!
I am trying to analyze my RNA-Seq data in a two factor experiment. The first is the strain: wild type (WT) and temperature sensitive (TS), and the second is the temperature at which they were grown: 25C and 37C. How would I get the fold change between WT 25C and TS 37C while controlling for differences due to strain and differences due to temperature? Am I correct in assuming I am looking for an interaction effect?
NOTE: I have been using the HISAT2 -> Stringtie -> Ballgown pipeline but couldn't figure out how to do it.
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