Hello to all, I have expression data from micro array affymetrix, i want to analysis the DEG could you help which R package is suitable for DEG analysis and also tell me a tutorial and script step by step because am beginner in this filed.

Thanks for your help

Ali

Hey Ali, it would help if you elaborated on the data that you currently have - presumably, you have obtained CEL files, but, do you know which specific array platform and version it is? Knowing the platform is important due to the fact that the Affymetrix arrays differ in their design. For example, some platforms cannot be pre-processed with the traditional affy package, and instead require the oligo package; however, oligo should now cater for all Affymetrix array designs and, for all intents and purpose, be the sole package used.

A general workflow proceeds as follows:

1. Data import, pre-processing, and QC (primarily oligo)
2. Differential expression analysis (limma)

A pretty good end-to-end workflow can be found here:

• An end to end workflow for differential gene expression using Affymetrix microarrays

Other useful resources:

• oligo User's Guide

Kevin