Closed bolak92 closed 11 months ago
Hi @bolak92, What is the data input you are working with? This does look strange.
It is MaxQuant global proteomics data. we have several samples from tissue and cells, diseased and normal. the grouping is then defined accross those 4 different groups.
Hello, I found the mistake at my part of the code, while I was averaging across technical replicates. It now works properly, so I will close this issue. Thank you for your help and understanding.
Hi @bolak92 , Thanks for letting us know!
Hello,
I tried to run the normalization methods comparison and got the following results back:![image](https://github.com/ByrumLab/proteoDA/assets/49613273/9e2b2955-77e9-414c-b4af-96f74f1a9656)
the vsn results look very different than I would expect and the ranges are freakily large. Is there an idea why that could be the case?
Also, the other plot looks weird with the logFC values that go to +- 100 ?![image](https://github.com/ByrumLab/proteoDA/assets/49613273/4e380f94-a18d-4682-bc67-4ddf7cb4a14f)
Thank you for your help and insights.