Datasets
Icebreaker survey
Download the instructional dataset:
The main data set for use in lectures is split into 5 tables. The idea of this dataset is that there is a randomized controlled trial of a drug aimed at reducing HIV risk by reducing inflammation. There were 23 participants in the placebo arm and 21 in the treatment arm. There were 3 visits for the trial – baseline (before any treatment occurred), week_1 (1 week after treatment) and week_7 (7 weeks after treatment). At each time point inflammation was measured using luminex (elisa_cytokines table) and immune cells counts were measured from a pap-smear (flow_cytometry table).
pid – participant id
time_point – “baseline”, “week_1”, or “week_7” arm – “treatment” or “placebo”
sample_id – the “wet-lab” sample id associated with this timepoint
pid - participant id
arm - “treatment” or “placebo”
smoker - “yes” or “no”
age – integer age in years
education – 4 options (“less than grade 9”, “grade 10-12, not matriculated”, “grade 10-12, matriculated”, “post-secondary”)
sex – all participants are “F”
pid – particpant id
time_point – “baseline”, “week_1”, or “week_7”
arm – “treatment” or “placebo”
nugent_score – Nugent Score, a number from 0-10. 0-3 is no BV, 4-6 is intermediate BV, and 7-10 is BV . crp_blood – decimal number representing C-reactive protein blood test (CRP) ph – vaginal pH
sample_id - the “wet-lab” sample id associated with this timepoint
cytokine - “IL-1a”, “IL-10”, “IL-1b”, “IL-8”, “IL-6”, “TNFa”, “IP-10”, “MIG”, “IFN-Y”, “MIP-3a”
conc – decimal number representing concentration
limits – either “within limits” or “out of range”
sample_id - the “wet-lab” sample id associated with this timepoint
All other columns – the integer count of this type of cell in this sample
cd4_t_cells might best be analyzed as a proportion of cd3_t_cells…