How to process gene expression data from Affymetrix U133 Plus 2.0 in Python

Question

[nkabo]

Hello,

I have a gene expression dataset taken from ArrayExpress based on Affymetrix U133 Plus 2.0. Is there a workflow that describes how to complete the steps below:

1) Replacing probe IDs with gene names, 2) Removing the probes which are not specific to only one gene 3) Getting the mean of expression value of multiple probes corresponding to one gene

Thanks in advance

Answer 1

[ATpoint]

Don't do that in python. Use established R packages to analyse microarrays. See this tutorial.

[nkabo]

Thank you for the reply. I had used the workflow and I expected to have approximately 26k data points but it ended up with over 48k probes. Is it expected or did I do something wrong during processing?

[Kevin Blighe]

The Affymetrix U133 covers a broad range of transcript types, including both coding and non-coding.

To figure out coding versus non-coding, perhaps you can get some ideas from here: A: Affymetrix Human Genome U133 Plus 2.0 Array