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yafeng / DEqMS

DEqMS is a tool for quantitative proteomic analysis
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Peptide counts for multiple label-free sample comparisons #15

Open potockym opened 1 month ago

potockym commented 1 month ago

Hello, I want to use DEqMS to analyze my LFQ dataset, which consists of five samples (each in triplicate) and analyze the DEPS among all ten possible comparison pairs. Should I use the values from the total dataset for the peptide min count, or should I always use minimum peptide counts relevant only for the compared sample pairs?
Thanks Martin Potocky

yafeng commented 1 month ago

@potockym Hi, I recommend to use minimum peptide counts relevant only for the compared sample pairs.

Yafeng