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hagenaue / bHRbLR_Enrichment_Stress_BehaviorAndHormoneData

Code used for the analysis of behavioral and hormonal data within the publication "Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype" by O'Connor, Hagenauer, et al.
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ReOutput All Results for Just RNA-Seq Animals #14

Open hagenaue opened 3 years ago

hagenaue commented 3 years ago

To determine how to package the results that we have into journal articles, it would be helpful to separately examine the behavioral and hormonal results for just the animals that had tissue included in the (much smaller) RNA-Seq experiment.

hagenaue commented 3 years ago

To output a version of the behavioral and hormonal results for the subset of animals included in the RNA-Seq experiment, you can use the ""sequencing ID" column in our master dataset, i.e., the one that we have already been using that is found here: https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/HRLR_EE_Stress_AllBehavData_forR_withNewCORTOxytIL6_SI_SDScoresFixed_FixedFormatIDs_TimeOnTop.csv

hagenaue commented 3 years ago

For re-outputting results, one source of trouble is going to be the fact that the RNA-Seq animals are almost entirely F53/F56 generation, so anytime there is generation included in a graph or an analysis the code may produce errors.

hagenaue commented 3 years ago

Another problem that may arise is it is possible that some of the variables may not have been measured for these animals (or for only a small number of these animals).

hagenaue commented 3 years ago

Ooooh - but there is another, bigger issue: Only bLRs were included in the RNA-Seq experiment.

...So I guess we are simply going to need to make an entire new repository of code (e.g., just copy this repository and tweak it) that is modified to fit the RNA-Seq animals, because we're going to need to remove bred Line from all of the graphs and analyses. Ah well.

hagenaue commented 3 years ago

The results for the RNA-Seq rats can be uploaded to MBox to the folder "Results_forRNASeqRats": https://umich.box.com/s/n5ve9ky4fwtfdoo5cgydl43m1e0pg3df