Closed kdaily closed 6 years ago
volcano plot, per brain region/study?
table/summary of expression levels as fxn of disease status
Using these datasets of summary statistics:
Unsure about what set of columns is required for uniqueness, looks like:
Model, Comparison, BrainRegion.ref, BrainRegion.ag, Gender.ref, Gender.ag, AOD.ref, AOD.ag, ensembl_gene_id, hgnc_symbol, logFC, CI.L, CI.R, AveExpr, adj.P.Val
But MSBB and ROSMAP do not have BrainRegion.ref
and BrainRegion.ag
columns.
@th1vairam is the person to answer this question
Here is a merged table from all three studies, 4 models with 7 brain regions and 4 comparisons https://www.synapse.org/#!Synapse:syn11180450
This is the code I used to do the above merge https://github.com/th1vairam/Brain_Reg_Net/blob/AMPAD_reprocessing/code/R/collateDifferentialExpressionResults.R
Done.
A forest plot of effect estimates for set of genes as a fxn of brain region/disease?