Identification of differentially expressed genes between different conditions

Question

[Sanches]

Hi everybody,

Let me ask you a question.

I have been trying to analyze my microarray data and I would like to use a few plots to show my results. In this case, what is the most frequent approach to explain differentially expressed genes? I mean, what should I show as a final result to have a simple and good article?

Thanks in advance

[Jean-Karim Heriche]

You should think about what the conclusion of your study is. A paper tells a story. What was the hypothesis you wanted to test ? What conclusion(s) can you reach ? The figures should be supportive of these so this defines how you're going to present your results.

[theobroma22]

This is a good point, and has been discussed in-depth in many forums as well as Biostars to date. From the OP's writing, hopefully I would assume, it seems he understands JKH's point. Overall, the logic is scientific in nature, in that you must demonstrate your hypothesis by working backward!

Answer 1

[theobroma22]

You could use the Limma package available on the Bioconductor website to do your analysis.