Fragile-X Bioinformatics Project

Question

[Francis]

Hey guys,

I'm looking for some advice. I have a project due in a couple weeks that needs to utilize python(and biopython) to create some sort of computational biology tool that will be used to analyze either GEO samples, DNA sequences, etc.

I plan on creating a program that will analyze GEO samples of Fragile-X patients, but don't really know what else I can do.

Any suggestions? I don't work in a lab and therefore don't have much experience with this. ANY suggestions would help

Please and thanks!

[Sean Davis]

Hi, Francis. A first step is to define hypotheses to test. To put it another way, you need to determine the questions you want to try to answer. Perhaps you can clarify above, as "analyze GEO samples" is not a hypothesis to test....

[Francis]

Yeah that is what Im trying to get at. I understand that 'analyzing GEO samples' refers to gene expression data, but WHAT exactly does that data show? What I could I make it show?

Answer 1

[Sean Davis]

Unfortunately, you'll need to decide the answer to those questions yourself. To start, you'll want to read the paper associated with the GEO dataset. Once you have decided what the data show and what questions you want to answer, you can move forward.

As a side note, I would not use python to analyse microarray data but would use R/Bioconductor or another software for microarray data analysis. Python is not a problem, but there is no need to reinvent wheels.