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BridgesLab / CushingAcromegalyStudy

The source code for the cushing and acromegaly studies, currently ongoing
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Check if age is a confounding factor between methylation and expression #31

Closed qtran1 closed 9 years ago

qtran1 commented 10 years ago

Put age in the model to see its effect. Cannot work on the methylation data until get the methylation for each sample.

davebridges commented 10 years ago

@innharvey mentioned this was brought up by a few people at her poster presentation. I'd like the three of us to talk about whether we should incorporate age/BMI/HOMA-IR into the differential expression models as well.

On Sun, Jun 29, 2014 at 11:21 AM, Quynh Tran notifications@github.com wrote:

Put age in the model to see its effect.

— Reply to this email directly or view it on GitHub https://github.com/BridgesLab/CushingAcromegalyStudy/issues/31.

qtran1 commented 10 years ago

Sure. But from the univariate analysis, I don't think BMI and HOMA-IR would play a role, but won't hurt to try.

qtran1 commented 10 years ago

The new analysis for acromegaly adjusting for age is done. We compared the effect of acro to control on gene expressions at two age groups (40,60] and (60,100]. The results are in data/processed/Annotated_Results_GRCh37.74_Acromegaly_age.csv and data/processed/GSEA_Results/Age_adjusted.

davebridges commented 9 years ago

For Acromegaly, are we ignoring patients under 40 for the age stratifying analysis? Basically are the groups 40-60 and 60+ or under 60 and over 60?

qtran1 commented 9 years ago

Right now, it's 40-60 and 60+. Let me think a bit more to see if we should clump the rest to <60 group.

qtran1 commented 9 years ago

GSEA results for the analysis of breaking age into 2 groups <60 and >=60.