proteotypic.only = T - Githubissues

vdemichev / diann-rpackage

Report processing and protein quantification for MS-based proteomics

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proteotypic.only = T #2

Closed oliverschilling closed 3 years ago

oliverschilling commented 3 years ago

Hello; thank you for this excellent script! I have just tried "unique.genes <- diann_matrix(df, id.header="Genes", quantity.header="Genes.MaxLFQ.Unique", proteotypic.only = T, pg.q = 0.01)" first with "proteotypic.only = T" and then with "proteotypic.only = F". The output was identical...what am I missing here?

thanks

Oliver

vdemichev commented 3 years ago

Hi Oliver,

Genes.MaxLFQ.Unique is always calculated by DIA-NN using proteotypic peptides only, so no difference here. Also, the diann_matrix function just takes the maximum value of quantity.header matching the id.header, so in this case it does not really calculate anything but just creates a matrix out of the list of identifications. So everything is working as expected.

Vadim

oliverschilling commented 3 years ago

Thanks!