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BridgesLab / CushingAcromegalyStudy

The source code for the cushing and acromegaly studies, currently ongoing
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Interaction p-value #37

Closed davebridges closed 10 years ago

davebridges commented 10 years ago

Is the interaction p-value for Cushings in this file the padj column or something else?

"../data/processed/Annotated_Results_GRCh37.74_Cushings_bmi.csv"

colnames:

"baseMean.CushingvsControl"
"log2FoldChange.CushingvsControl" "lfcSE.CushingvsControl" "stat.CushingvsControl"
"pvalue.CushingvsControl" "padj.CushingvsControl" "baseMean.Obese_vs_Overweight"
"log2FoldChange.Obese_vs_Overweight" "lfcSE.Obese_vs_Overweight" "stat.Obese_vs_Overweight"
"pvalue.Obese_vs_Overweight" "padj.Obese_vs_Overweight" "baseMean"
"log2FoldChange" "lfcSE" "stat"
"pvalue" "padj" "external_gene_id"

qtran1 commented 10 years ago

Yes, padj is the interaction p-value

davebridges commented 10 years ago

Ok so when you rerun the GSEA can you sort that group by logfc of the interaction rather than the pvalue because in this case the slope direction will matter

On Thursday, August 7, 2014, Quynh Tran notifications@github.com wrote:

Yes, padj is the interaction p-value

— Reply to this email directly or view it on GitHub https://github.com/BridgesLab/CushingAcromegalyStudy/issues/37#issuecomment-51552832 .

qtran1 commented 10 years ago

GSEA on the whole Cushing's data with BMI and disease interaction has been rerun using log2FC as the ranking criteria. This results replaced the old results and were pushed to github. GSEA for Reactome was also included.