Use for transformation before Differential Analysis

[annabel-dekker]

Dear Ruth,

I'm very interested in your package, but please consider I'm pretty new to the topic.
We were conceptually thinking about some utilizations...
I understand that the registration of the expression data can be used to ultimately identify genes that follow a similar regulatory pathway and vice-versa. Of course, the registration itself stretches gene expression datapoints that were found to be 'registerable' and 'comparable' into registered gene expression data.
We were arguing that before performing differential gene expression between similar species over time - but from different varieties - would it make sense to first register their gene expressions over time? I can imagine this would avoid false positive differential genes, which would have show up purely because of the delay of the expression patterns. Did you test this, and would registered gene expression be compatible with either edgeR or DeSEQ2?

Happy to hear from you,
Annabel

[ruthkr]

Hi Annabel,

Thank you very much for your questions and for your interest to my package.

We actually have not thought about integrating the package to either edgeR or DeSEQ2, but this can be potentially a great added feature to the package. What my package can do currently is to identify whether pair of genes have the same dynamics or not.

However, depending on whether you scale your expression or not, you may be able to get additional information whether pair of genes have same dynamics + not differentially expressed over time if they can be registered with both "without scaling the data" and "with scaling the data". So, this would allow us to identify which differentially expressed genes can be explained by a simple shift and stretch of the data vs which differentially expressed genes actually have also different dynamics.

Thank you for the suggestion. I will look into how best to do this. If you have a specific dataset you’d like help with, do get back to me. I would be happy to try to help.

Best wishes,
Ruth

[annabel-dekker]

Thanks for your reply!
I fully agree this would be very interesting. We are also currently looking into this, will reach out if needing help!
Thanks a lot,
Annabel