I want to use global test.

Question

[dxodnd]

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.

[ATpoint]

I think it is bad practice to keep two communitites busy with the same question, https://support.bioconductor.org/p/9136105/

Answer 1

[Istvan Albert]

Use the globatest in R, follow the vignette

https://www.bioconductor.org/packages/release/bioc/html/globaltest.html

When it comes to more advanced statistical models you won't find those implemented in Python. Then you can fool around in rpy, but all you'll get is the worst from both worlds.

The R skill requirements for this package are pretty low, you'll spend far more time fighting needless problems if you want to do it in Python.

Learn a little R and you do yourself a favor that will pay off many times over in the future.

[dxodnd]

The data that I use is notification is GPL96.

Should I run it like gtKEGG (set, plz_gt, id = "pd.hg.u133.plus.2")?