DATA:

We have a set of breast cancer patients and a set of healthy samples. We want to know which genes are involved in the development of the disease. For that, we want to perform a differential expression between both groups.

The experimental design file includes information about to which class belongs each sample.

• Expression file: brca_demo_counts_4babelomics.txt
• Experimental design file: brca_normal-basal_ed.txt

EXERCISE:

1. Upload the expression file to Babelomics
2. Go to Processing → Edit → Edit your uploaded data
3. Press on “File browser” and select the file. Press OK
4. Add a new categorical attribute called “Class”, and give to each sample the class specified in the experimental design file above. Press “Save changes”
5. Go to Expression → Differential Expression → RNA-Seq Class Comparison
6. Select the data you just edited
7. As class to analyse select the variable “Class”, and compare “Tumor” vs. “Normal”
8. Normalize with TMM
9. Set ultiple-test correction to Benjamini-Hochberg
10. Set adjusted p-value to 0.05
11. Launch job

QUESTIONS:

1. Which are the 5 most differentially expressed genes?
2. Download the table of results and heatmap.