Batch correction for protein data

Question

[4732b159]

Hello,

I wonder what tools people use and suggest for batch correction of GeoMx DSP protein data.

Thanks for all suggestions :)

Answer 1

[ATpoint]

Same as for any other analysis with tagged tools, include it into the model. See the user guides for details.

[4732b159]

Hi, many thanks for your response :) would you elaborate how you would do this I am not quite sure yet and I am normally use deseq2 for DEG analysis but how is it possible to include batch correction into my model? or do you use extra tools for this? thanks for your suggestions!