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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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How to quantification with enriched samples (con vs exp) #961

Open Lang5991 opened 8 months ago

Lang5991 commented 8 months ago

Dear vdemichev, I have two enriched sample groups, the con group and exp group. Generally, con group has less protein while exp group can enrich more. So protein abundance varied greatly between the two groups. Then how can I quantificate using DiaNN？Does it need to be normalized, and how? Looking forward to your response.

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vdemichev commented 8 months ago

It's probably a good idea to keep DIA-NN's normalisation enabled, but also worth checking if further normalisation at the protein level will be beneficial. This can be done with quite a simple script in R or Python, e.g. select robustly detected proteins and normalise by their medians.

Lang5991 commented 8 months ago

It's probably a good idea to keep DIA-NN's normalisation enabled, but also worth checking if further normalisation at the protein level will be beneficial. This can be done with quite a simple script in R or Python, e.g. select robustly detected proteins and normalise by their medians.

Thank you for your kindness!