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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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Re-output All Results for Just Proteoglycan ISH animals #13

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) proteoglycan in situ hybridization (ISH) experiment (vs. the animals that did not have tissue included in the ISH experiment).

hagenaue commented 3 years ago

To output a version of the behavioral and hormonal results for the subset of animals included in the proteoglycan in situ hybridization (ISH) experiment, I've uploaded a spreadsheet of ISH data that is formatted so that it is in the exact same order as our master data spreadsheet (i.e., should be perfectly aligned with our current dataset): https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/ProteoglycanISH_ForComparisonWBehav.csv Hypothetically, I believe you should be able to use this spreadsheet to subset our behavior/hormone data frame within the "01_ReadingInData" code (https://github.com/hagenaue/Angela_HRLR_StressEnrichData/blob/master/01_ReadingInData.R) to only include animals with ISH data and then re-run the rest of the code. Note - I do not recommend actually joining the ISH dataset with our current behavioral/hormonal data frame, because much of the rest of our code has the variables (sadly) defined using column numbers - if the column numbers shift due to adding in the ISH data, the rest of the code is going to break. :(

hagenaue commented 3 years ago

For re-outputting results, one source of trouble is going to be the fact that the ISH animals are almost entirely F49 generation, so anytime there is generation included in a graph or an analysis the code may produce errors. Hopefully it will still run, otherwise we may need to make a modified version of the code just for the ISH animals that doesn't include generation.

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), e.g. hormones, video analysis. Again, hopefully the code as we have it will still run, otherwise we may need to make a modified version of the code for just the ISH animals.

hagenaue commented 3 years ago

The newly re-outputted results for the proteoglycan ISH rats can be uploaded to the "Results_forProteoglycanISHRats" folder on MBox: https://umich.box.com/s/avdmy9c2rp8ubbrr9nmtsbu9ziepuwl1

hagenaue commented 3 years ago

The newly re-outputted results for the non-proteoglycan ISH rats can be uploaded to the "Results_forNonProteoglycanISHRats" folder on MBox:https://umich.box.com/s/96xwwgr1s6xj6amvenvv6hceaq3zikl2