I am a PhD student working on developing ideas for my dissertation papers. One of my planned papers will be working with some (human) gene expression data.
I have had a class on working with gene expression data, but no practical experience. From what I remember from my project in that class, you do a bunch of pre-checks and QC, then you remove batch effects, then you summarize expression across probes and normalize. I thank that part of my class project took me about three days.
But when I talk to other people about it, they say that cleaning/QCing/normalizing gene expression data is really hard, that it will take forever to get it working, and that if I do this dissertation paper I am going to end up taking extra years to graduate.
Am I missing something here? Why do the people I talk to seem to think this is so hard and time consuming -- is it really that bad? Should I avoid having a dissertation paper that uses gene expression data if I want to graduate on time?
(The data will be from Affymetrix microarrays. There are enough samples to use two 96-well plates, so batch effects will be more of a concern than they were in my class project.)