Regarding to Two-color microarray data analysis (DGE)

Question

[SHIRUI]

HI dear friends

How should I do DEG analysis based on Two-color microarray data(GSE24230), and from database,I have gotten ratio such as log2(treatment/control) and log2(control/treatment) (Dye-swap experiment).

So how should I do DEG analysis based on these data

Thank you so much

[Ram]

Please do not use bioinformatics as a tag unless your post is about the field of bioinformatics itself. For proper examples, please see Forum and News type posts under https://www.biostars.org/tag/bioinformatics/

I've removed the tag this time but please keep this in mind for future posts.

Answer 1

[ATRX]

Use a bioconductor package called limma for normalization, correction of Dye swap effect and then differential expression analysis. Here is the link to the package: https://www.bioconductor.org/packages/release/bioc/html/limma.html