Question: How to process gene expression data from Affymetrix U133 Plus 2.0 in Python
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gravatar for nkabo
8 months ago by
nkabo10
nkabo10 wrote:

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

ADD COMMENTlink written 8 months ago by nkabo10

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

ADD REPLYlink written 8 months ago by ATpoint29k

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?

ADD REPLYlink written 8 months ago by nkabo10
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