Microarrays

A few years ago I gave up on a PhD in Molecular Biology and settled for an MS. Then I switched to a more applied field of study. It's going ok I guess, but MolBiol is still my first love. Last year my current PI collaborated with another lab to do a microarray study. He did not want me to have anything to do with it, because it would distract too much from my current project, and right he was. However, where do you find somebody who is comfortable with both expression data *and* our system?

My PI asked me if I knew anybody who could analyze the data. Hmmm. Well, I could really only think of one person in this neck of the woods and it would be... me. He was reluctant and said he would ask someone else for advise, but the second and third (and possibly fourth) person he asked referred him back to me. It took him a full 6 weeks, but unable to do it himself, he handed over the disks and asked me if I could take a look at the data. It was all I could do to not climb on the roof and let the world know that I'd be looking at the data. How cool is that! I didn't let on though and casually said that I would try and make some time to look at the data.

The first time I tried to open one of the files my 7-year old laptop crashed. Subsequent times weren't more successful, so I had to resort to something more capable of opening Excel files that were a little on the large side. Several days later I finally managed to lay claim to the lab computer (being a parent does not often allow me to go back to the lab late at night), and open a file. It took several minutes to even open. Scrolling down and to the right and back up and to the left. Numbers, lots of numbers. A few labels and more numbers. I closed the file and opened another one. Same result. I was kicked off the computer by the lab manager who had something to do. So much for my first glimpse at the data.

It took me a few days before I dared open the file again. Where to start? There are so many numbers! In retrospect I am the lucky one. Someone else got to do all the dirty work. The RNA isolation, reverse transcription into cDNA, labeling, hybridizing, all that good stuff. Better yet, someone else did the statistical analysis. All I have to do is interpret it. Should be easy right? But staring at hundreds of genes being differentially expressed is a bit overwhelming. Scratch that. *Very* overwhelming.

For several weeks I did not open the files again. I just mulled it over and over in my mind. Trying different ways of looking at the data, hoping something would jump out at me. There is no way my PI is going to pay for me to attend some kind of fancy conference to learn something about this. I'm on my own here. Re-inventing the wheel. I chopped the files up in smaller pieces so I can now manage them even on my ancient laptop. Then I started sorting and re-sorting the data. Just making different lists. To be continued....