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saezlab / dorothea

R package to access DoRothEA's regulons
https://saezlab.github.io/dorothea/
GNU General Public License v3.0
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Integration of regulon activities across different datasets #39

Closed GMFranceschini closed 3 years ago

GMFranceschini commented 3 years ago

Dear authors, thank you for developing dorothea, I am excited to use it for my research. I would like to ask a question concerning the integration of different datasets to compare regulon activities, I hope this is the right place.

Besides merging all the data during the upstream processing, is there a strategy to compare the NES obtained in a dataset with another one? Something tells me that I cannot directly do that, can you confirm?

For instance, I found the regulons reported in https://dorothea.opentargets.io/#/ very useful, and I would like to measure and compare regulons the activity in another set of samples (and then for example find the most similar cell line). But let's suppose I now measure the same regulons on a set of immune cells, could I integrate the NES of those two sources? What would be your recommendation to achieve that, possibly starting from processed data?

christianholland commented 3 years ago

Hi @GMFranceschini, please apologise the delayed reply. Following the vignette the run_viper()function scales the expression matrix. This makes two independent matrices of NES hardly comparable. To make them directly comparable I recommend to merge all data before computing the NES.

GMFranceschini commented 3 years ago

Thank you, Christian. So you suggest integrating counts data and run the analysis of the full set. That was more of a viper question probably, sorry for that. Closing the issue, feel free to reopen if you ever stumble upon another strategy!