> DDA2009.proposed <- MSstats::dataProcess(raw = fileData1,
+ normalization = 'quantile',
+ summaryMethod = 'TMP',
+ censoredInt = "NA",
+ MBimpute = TRUE)
INFO [2022-03-08 10:48:00] ** Multiple fractionations exist: 2 fractionations per MS replicate.
INFO [2022-03-08 10:48:57] ** Features with one or two measurements across runs are removed.
INFO [2022-03-08 10:48:57] ** Fractionation handled.
INFO [2022-03-08 10:48:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
Error in dcast.data.table(input[nonmissing_filter & label_filter & (RUN %in% :
Can not cast an empty data.table
Error in .handleFractionsLF(input) :
** It is hard to find the same fractionation across sample, due to lots of overlapped features between fractionations. Please add Fraction column in input.
normalization = 'quantile'parameter in the dataProcess() will report an error like below, and there is no error if use the default parametersnormalization = 'equalizeMedians'.Data can be downloaded from here.
Data can be downloaded from here.