Hi

I am a novice for RNA Seq data analysis, and I am trying to compare groups which belong to more than 2 groups. I am unsure whether I have to specify this in 'DGEList' function or the 'exactTest' function, and how exactly to specify this?
For example it may have 3 categories : Tumour_typeA, Normal, Tumour_typeB with each sample belonging to 1 of these. If I now want to find differentially expressed genes between Tumour_typeA and Tumour_typeB (and skip the 'Normals' ), where can I specify this.

Any advice or help you can provide will be very helpful.



Thanks

Sakshi


Sakshi Gulati
PhD Student
Biomolecular Modelling Laboratory
Cancer Research UK London Research Institute
44 Lincoln's Inn Fields
London WC2A 3LY


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