Hello, I want to get the p-value of each probe through a global test with the data in https://github.com/Foreist/dummy-data .

The data source for the above address is https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13351.

I selected a specific probe and normalized it with python.

I inevitably have to use rpy, but even if it doesn't, I'm curious how to apply that data to the global testing technique even through r.

I mostly use Python, so I'm not familiar with r.

There is really no place to ask.

You can also recommend an example.

Thanks for reading.

Dear Kim,

I understand that you're just getting started with expresson analyses, but I think that you're on the wrong track in several ways:

1. globaltest (the Bioconductor package) does not give p-values for individual probes. It is only for gene sets.

2. You can't normalize an individual probe in isolation. All the probes need to normalized together. The GSE data series you link provides normalized expression values, so there is no need to you to re-normalize the values.

3. This forum is only for Bioconductor R software. Bioconductor provides functionality that is not available in any Python package.

4. There are many Bioconductor guides describing how to analyze Affymetrix data. Probably the easiest would be to download the normalized expression values from GEO and plug them into a limma package analysis.