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Vitek-Lab / MSstats

R package - MSstats
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Bug in merging fractions #65

Closed mstaniak closed 2 years ago

mstaniak commented 3 years ago

https://github.com/Vitek-Lab/MSstats/blob/master/R/utils_normalize.R#L280 this line: we test for an error, but dcast never throws it - if there are duplicated values, there's just a warning. What should we test? if any value is larger than 1? @MeenaChoi

daichengxin commented 2 years ago

Hi mstaniak @mstaniak , I encountered the same problem when running dataProcess(). This my data: https://github.com/daichengxin/shared/blob/main/out_msstats_tech.csv. Technical replicate column is added. How to solve this problem？ Thanks

daichengxin commented 2 years ago

image Does technical replicate seem to be problematic?

mstaniak commented 2 years ago

Hi,

thanks for providing the data, I will let you know what the issue is this week

mstaniak commented 2 years ago

@daichengxin quick question: do you have a separate ID for each run? Most importantly, for each of the technical replicates. Sorry I couldn't take care of this earlier

mstaniak commented 2 years ago

@daichengxin candidate solution:

devtools::install_github("Vitek-Lab/MSstatsConvert", ref = "hotfix-techreplicate")
devtools::install_github("Vitek-Lab/MSstats", ref = "hotfix-fractions-check")

Please re-run your analysis after installing these updates and let me know if it's OK now

daichengxin commented 2 years ago

@daichengxin quick question: do you have a separate ID for each run? Most importantly, for each of the technical replicates. Sorry I couldn't take care of this earlier

Yes, have a separate ID for each run and technical replicates. This is the result of my re-run. I'm not sure if this works properly. image

mstaniak commented 2 years ago

It's almost OK. The "Aggregate function missing" warning should not happen after installing MSstats from hotfix-fractions-check branch, I will double-check this. I will also check the way technical replicates are counted for logging purposes