Thursday, May 31, 2007

Arrays and more arrays

Don't get me wrong. I absolutely love going through sequences and trying to find patterns. And like Sandra Porter, I love analyzing sequences. But I have been working for months on thousands of sequences, and right this moment it is getting a bit much. Taking this break should help. I promised my adviser I would get the next step of my analysis back to him late last week, and I'm still working on it. It didn't help that one of my files got corrupted while I was saving it to my departmental server, and I lost hours and hours of work. Messing up an enormous spreadsheet was probably not a good idea either, I've spent an entire day cleaning up that mess.

I don't have any software available to analyze this data quickly for me. Someone else in my department told me I could try and use the program for which he is getting a one-year license. But he wasn't sure himself what the software would do, and therefore couldn't tell me whether it'd be useful.

So, I'm doing it by hand. Data from 8 slides with each about 44,000 genes on it. Granted, not all of them are differentially expressed, in fact not even close to all of them. But still, it's a respectable amount of work.

Well, at the very least it's pushed dementors far from my mind today. I'm guessing I have at least a couple more hours of work to do on this phase. And then I should be able to submit to my adviser a list of genes that we might consider looking at in more detail. He wants to submit a research proposal based in this information by July, so I'd better get back to work now.

If I've bored you, sorry, but this blog is more for me than for anyone else.

P.S. If anyone knows of any amazing, relatively inexpensive software to make my analysis of microarray data easier, this would be a great time to leave a comment here. Basically, the statistics has been done, I just need to make sense of the data, and maybe display the lot in a visually appealing way.


Sandra Porter said...

Well, I do know some software that might be of help.
But, I am potentially biased since the guy who developed it now works for us.

Anyway, you should listen to one of their webinars and try a trial account. The info is here: Genesifter.

makita said...

Thanks for visiting Sandra. I will definitely listen to a webinar (that's a new word for me). Sounds exciting. By the way, I loved you sequence analysis post. Sequence analysis is my first love.