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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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UpdatingAnalyses_FollowingCleanedOpenFieldUSVData #16

Open hagenaue opened 3 years ago

hagenaue commented 3 years ago

1) Review where we left off for the analyses of...

A) The full behavioral and hormonal dataset: https://umich.box.com/s/ejwub6sexjcxy8c43pw56nbpjq00k64z

B) The subset of animals included in the proteoglycan in situ hybridization experiments. https://umich.box.com/s/5olt9fgbpt3eu1rtc2ra97v2lbgofyf0

Highlight any methods & results related to the open field task (Distance and %time in center) or USV measurements ( or all variables together including these)

hagenaue commented 3 years ago
  1. Updating the results for the proteoglycan paper to include the updated open field data:

A) Review the code associated with the subset of animals included in the proteoglycan in situ hybridization experiments (single code document): https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/21_OnlyProteoglycanAnimals.R

B) The updated dataset is located here: https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/HRLR_EE_Stress_AllBehavData_forR_withNewCORTOxytIL6_SI_OFSDScoresFixed_FixedFormatIDs_TimeOnTop_forProteoglycan.csv

C) Re-run the parts of the code related to the open field (distance, time in center) or that include any processing of the full dataset.

hagenaue commented 3 years ago
  1. Updating the results for the full behavioral and hormonal dataset to include the updated open field data and USV data - it may need to be me (Megan) that does this:

A) Review the code (almost this entire repository...sigh) and identify which sections include the open field task (Distance and %time in center) or USV measurements in some manner and will need to be re-run.

B) The updated dataset is located here: https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/HRLR_EE_Stress_AllBehavData_forR_withNewCORTOxytIL6_SI_OFSDScoresFixed_FixedFormatIDs_TimeOnTop_forFullBehavior.csv

C) Re-run the parts of the code related to the open field (distance, time in center) or USVs or that include any processing of the full dataset. This is going to be a much bigger pain in the butt than re-running the code for the proteoglycan animals, because we should probably adapt the code to include some output for 1) the full open field time series, 2) different variations on the USV analyses, to provide justification for the final analyses. Meh.

hagenaue commented 3 years ago
  1. Ok, this is awful, but apparently the cleaned open field data included a mathematical error (my fault this time!) - the % time in centre was the sum of the % time in center for time bins minutes 2-5 instead of the average. I have now fixed this and uploaded the updated datasets here:

Full dataset: https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/HRLR_EE_Stress_AllBehavData_forR_withNewCORTOxytIL6_SI_OFSDScoresFixed_FixedFormatIDs_TimeOnTop_forFullBehavior2.csv

Dataset just for proteoglycan ISH animals: https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/HRLR_EE_Stress_AllBehavData_forR_withNewCORTOxytIL6_SI_OFSDScoresFixed_FixedFormatIDs_TimeOnTop_forProteoglycan2.csv

... it doesn't change any of the results, but it will change the y-axis on the graphs... which means re-outputting everything again. :(