DATA:

We have a dataset in which we have measured the expression profile of two different organs in healthy mice. We have 5 technical replicates per organ: l1-l5 corresponding to Liver, and k1-k5 corresponding to Kidney.

Before working with the data set we want to normalize it to correct for possible biases.

• Expression file: rnaseq_difexp.txt
• Gene length file: gene_length.txt

EXERCISE:

Normalize the expression file above in the 3 following ways:

1. Use gene length file and set Automatic method
2. Use gene length file and set RPKM method
3. Set TMM method without using the gene length file

Compare the different results.

• Which method is the best one?
• What differences do you find?