Exercises: Organizing workflows I

Go to parent Introduction to R/Bioconductor for analysis of microarray data#Training Units

Atxn1

Adapt the workflow for the estrogen data from the tutorial and run it for the Atxn1 data.

Modified data

Modify the workflow so that the sample with CEL file high10-1.cel is not included. What changes need to be made?

Modified workflow

Make the following changes to the workflow:

• Add a boxplot of the raw data.
• Include KEGG pathways into annotation for the candidate genes.
• Replace the MA plot with a volcanoplot
• Put nicer labels on the axes in the volcano plot.
• Export the list of candidate genes to a text file instead of a HTML file.
• Save the expression set (eset).
• Generate a heatmap of the top-300 regulated genes into the workflow.

Run the workflow on the Atxn1 data.

Bonus: define a prefix string at the top of the workflow, like "estro" for the estrogen data or "Atnx1" for the data here, and add the prefix to all the filenames generated within the workflow.

Golub

Modify one of the existing workflows so that it works with pre-defined expression sets, and use it to run the analysis on the Golub data.