This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Fragile-X Bioinformatics Project

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!

microarray biopython geo structural python
• 2,627 views • link
updated by Sean Davis Sean Davis • written by Francis • Francis

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....

• 0 views • link
written by Sean Davis Sean Davis

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?

• 0 views • link
written by Francis • Francis

1 answer

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.

• 2 views • link
written by Sean Davis Sean Davis

Log in to answer this question.

More posts like this