1 Assessment

This session is assessed using MCQs (questions highlighted below). The actual MCQs can be found on the BS1070/MB1080 Blackboard site. The deadline is listed there and on the front page of the BS1070/MB1080 blackboard site. This assessment contributes 5% of module marks. You will receive feedback on this assessment after the submission deadline.

2 Getting the data into R

There are lots of ways of getting data into R. Its one of the most annoying things about it as a beginner. But I’m assuming everyone is using Rstudio, so I’ll show you how I get data in when someone gives me a csv file.

  1. Look at the right hand top window in Rstudio. See the Import Dataset. Use this to import the data as textfile or From Text (base) in newer versions. Make sure that the heading option is on.
  2. Notice what you really did was displayed in the console.
celldata <- read.csv("~/Dropbox/Teaching/first_year_stats/sessions/8.mb1080/celldata.csv")
  1. That means if you typed that into the console you would get the same effect (with your filepath not mine).
  2. Have a look at the data it should have 120 observations of 3 variables.

3 Data analysis for hand-in

In this study you are comparing three different genotypes to test if these genotype (AA, Aa and aa) influence the endothelial cells ability to bind to monocytes. To generate reliable data you will have repeated the experiment a number of times. The data generated includes 40 repeats.

In the analysis of this experiment you are asking two questions:

  1. Does the genotype have an effect on the amount of bound THP1 cells in normal physiological conditions (variable:normal)?
  2. Does the genotype have an effect on the amount of bound THP1 cells after prior stimulation with the cytokine TNFα (variable: TNFa)?

A good general framework for any analysis is Plot -> Model -> Check assumptions -> Interpret -> Plot again. We will follow this below.

3.1 Analysis for today

For each of the two variables, I need you to

  1. A quick explore of your data (maybe skimr or summary if you are having problems with skimr) and a boxplot to quickly check if species has an effect
  2. Carry out an ANOVA
  3. Check the assumptions of your model (autoplot)
  4. If significant and assumptions are met, do a tukey test, otherwise carry out a Kruskal wallis and then a dunn’s test
  5. A final plot (pretty boxplot?)

4 MCQs

  1. Does genotype have an effect on the amount of bound THP1 cells in normal physiological conditions(with correctly reported statistics (either parametric or nonparametric are fine))?
  2. If yes, which genotypes are different in normal physiological conditions (with correctly reported statistics)?
  3. Does the genotype have an effect on the amount of bound THP1 cells after prior stimulation with the cytokine TNFα (with correctly reported statistics (either parametric or nonparametric are fine)?
  4. If yes, which which treatments are different after prior stimulation with the cytokine TNFα (with correctly reported statistics)?