Exercise 1 - Task 1
Gene expression analysis: GEO (Gene Expression Omnibus)
1.1.1 Retrieve gene expression data from GEO
Istructions
-
This exercise task will guide you through retrieving and preprocessing a DNA microarray dataset in
R
using the
GEOquery
and
dplyr
packages.
-
You will perform data, loading, reformating, filtering
using an integrated development environment (IDE) called
RStudio.
A cheat sheet describing the RStudio IDE can be downloaded from
here).
-
To reproduce the analysis, the documented task must be followed step by step, using the R commands
reported in the document.
-
To solve to some of the tasks posed at the various steps of the analysis,
you should implement a slightly different version of the preceding code following the instructions
and reading the function documentation (Hint: use the help window in Rstudio)
In case of difficulties, you can click on the "Toggle solution" button to reveal the code solution.
-
Please use on the following link to start the step-by-step exercise task:
Exercise 1 - Task 1.1.1
1.1.2 Load the data set using Genesis
Try sorting genes with different methods, to get a first impression of the expression profiles.
-
Which are the 4 genes with the highest and lowest mean expression over time
-
Which are the 4 genes with the highest and lowest variance over time
Links: