Create new MD with updated analysis - Githubissues

PNNL-CompBio / cytokineDrugResistance

Studying the impacts of cytokines on drug resistance in AML

MIT License

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Create new MD with updated analysis #1

Closed sgosline closed 2 years ago

sgosline commented 3 years ago

Start with MD 13 (doing the phospho analysis) with the following modifications:

1- remove all patients with Treatment='Trametinib Withdrawn' 2- Create PCA plots of global and phospho for the late molm13 only, and the late molm 13 + parental 3- redo KSEA analysis with p-values, and double check that correct parentals are used

tram vs parental (late only)
tram+mcp1 vs parental (late only)
tram vs. tram+mcp1 (late only) 4- output boxplot data as TSV 5- create heatmap of substreates of selected kinases () across all conditions

mdnestor commented 3 years ago

PCA plots are done but KSEA needs to be revised