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two errors about dataProcess() #85

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Douerww opened this issue Mar 8, 2022 · 0 comments
Open

two errors about dataProcess() #85

Douerww opened this issue Mar 8, 2022 · 0 comments

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@Douerww
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Douerww commented Mar 8, 2022

  1. Selecting the normalization = 'quantile' parameter in the dataProcess() will report an error like below, and there is no error if use the default parameters normalization = 'equalizeMedians'.
    Data can be downloaded from here.
> 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
  1. Using the dataProces() (default parameter) will report an error that never occurred, and I want to know what caused it so I can write it in my condition judgment statement. Error message is as follows:
    Data can be downloaded from here.
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.
@Douerww Douerww changed the title Error in dataProcess() and a new appeared error report two errors Mar 8, 2022
@Douerww Douerww changed the title two errors two errors about dataProcess() Mar 8, 2022
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