Hi,
What would comprise as best practices for comparing RNA-seq data from two species where you don't have many replicates. Can software like cuffdiff/edgeR be used when doing cross species differential expression analysis ( only taking the orthologus genes). Any suggestions would be appreciated.
Thanks
Do you have different conditions?
If so, one way to do this for orthologs is to compare the ratio/differential expression status of a gene across species. For example, DogGene1 and HumanGene1 are orthologs. DogGene1 is differentially expressed between Condition1 and Condition2, but HumanGene1 show similar expression (not differentially expressed) between Condition1 and Condition2.
The downside to that method, of course, is that it leads the unwary to compare p-values, which is a bad idea.
Depends on how accurate those are. The fewer samples you have the less meaningful fold-change estimates become.
You are correct, you need to have confidence in determining differential expression status. OP should make sure that he is able to determine differential expression within a species first (with confidence). It would be suspect to compare p-values across species. With this method you will end with a set of orthologs that show species co-expression (are DE in the same condition in both species), or show species specific differential expression (only DE in one of the species).
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Mapping genes across species and doing differential expression are 2 separate problems. cuffdiff, edgeR only solves the 2nd one. What species are you dealing with?
I have mapped the data. Now I just want to compare the expression. I want to know what are the better ways of comparing the data. I am dealing with Dog and Human.
I see, misunderstood your question..