Clustering data with heatmap algorithm for (Study ST003788)

This analysis uses the 'heatmap.2' function of gplots package in the R statistics environment


The rows are scaled to have mean=0 and standard deviation=1

Factors:

F1Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Alive
F2Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Dead
F3Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Follow-up < 60 days
F4Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Alive
F5Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Dead
F6Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Follow-up < 60 days
F7Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Alive
F8Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Dead
F9Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Follow-up < 60 days
F10Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Dead
F11Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Follow-up < 60 days
F12Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-positive | diagnosis:Non-infectious control | outcome_day_60:Dead
F13Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-positive | diagnosis:Non-infectious control | outcome_day_60:Follow-up < 60 days
F14Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Alive
F15Sample source:CSF | cohort:Indonesia | sex:Female | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Dead
F16Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Alive
F17Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Dead
F18Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Follow-up < 60 days
F19Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Alive
F20Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Dead
F21Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Follow-up < 60 days
F22Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Alive
F23Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Dead
F24Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Follow-up < 60 days
F25Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Alive
F26Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Dead
F27Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Follow-up < 60 days
F28Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-positive | diagnosis:Non-infectious control | outcome_day_60:Alive
F29Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-positive | diagnosis:Non-infectious control | outcome_day_60:Dead
F30Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Alive
F31Sample source:CSF | cohort:Indonesia | sex:Male | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Dead
F32Sample source:CSF | cohort:Indonesia | sex:Male | HIV:NA | diagnosis:Cryptococcal meningitis | outcome_day_60:Alive
F33Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Alive
F34Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Dead
F35Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Follow-up < 60 days
F36Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Alive
F37Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Dead
F38Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Follow-up < 60 days
F39Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Dead
F40Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Follow-up < 60 days
F41Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-positive | diagnosis:Non-infectious control | outcome_day_60:Alive
F42Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Alive
F43Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Dead
F44Sample source:CSF | cohort:Vietnam | sex:Female | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Follow-up < 60 days
F45Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:Alive
F46Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:Cryptococcal meningitis | outcome_day_60:Alive
F47Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Alive
F48Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Dead
F49Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:Non-infectious control | outcome_day_60:Follow-up < 60 days
F50Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Alive
F51Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Dead
F52Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-negative | diagnosis:TBM | outcome_day_60:Follow-up < 60 days
F53Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Alive
F54Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Dead
F55Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:Follow-up < 60 days
F56Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-positive | diagnosis:Non-infectious control | outcome_day_60:Alive
F57Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Alive
F58Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Dead
F59Sample source:CSF | cohort:Vietnam | sex:Male | HIV:HIV-positive | diagnosis:TBM | outcome_day_60:Follow-up < 60 days
F60Sample source:CSF | cohort:Vietnam | sex:NA | HIV:HIV-negative | diagnosis:Bacterial meningitis | outcome_day_60:NA
F61Sample source:CSF | cohort:Vietnam | sex:NA | HIV:HIV-positive | diagnosis:Cryptococcal meningitis | outcome_day_60:NA
Data matrix
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