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:
- Use gene length file and set Automatic method
- Use gene length file and set RPKM method
- Set TMM method without using the gene length file
Compare the different results.
- Which method is the best one?
- What differences do you find?