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ByrumLab / proteoDA

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Normalization comparisons dissimilar from the tutorial #250

Closed bolak92 closed 1 year ago

bolak92 commented 1 year ago

Hello,

I tried to run the normalization methods comparison and got the following results back: image

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

Thank you for your help and insights.

ByrumLab commented 1 year ago

Hi @bolak92, What is the data input you are working with? This does look strange.

bolak92 commented 1 year ago

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.

bolak92 commented 1 year ago

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.

ByrumLab commented 1 year ago

Hi @bolak92 , Thanks for letting us know!