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Vitek-Lab / MSstats

R package - MSstats
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Error message not clear #23

Closed wolski closed 6 years ago

wolski commented 6 years ago

I am trying to run:

 QuantData <- dataProcess(raw)

with all default parameters. This produces the following error message:

== Start the summarization per subplot...
Getting the summarization by Tukey's median polish per subplot for protein  iRT_Protein ( 1  of  13 )
*** error : can't summarize per subplot with TMP.

Therefore, I run

QuantData <- dataProcess(raw,summaryMethod = "linear")

Which does complete

But where do I find the plots the messages below are talking about?

Getting the summarization for censored missing values per subplot for protein  iRT_Protein ( 1  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|O95477|ABCA1_HUMAN ( 2  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|P02786|TFR1_HUMAN ( 3  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|P04406|G3P_HUMAN ( 4  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|P08195|4F2_HUMAN ( 5  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|P49281|NRAM2_HUMAN ( 6  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|P63104|1433Z_HUMAN ( 7  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|Q01650|LAT1_HUMAN ( 8  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|Q15043|S39AE_HUMAN ( 9  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|Q15365|PCBP1_HUMAN ( 10  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|Q9C0K1|S39A8_HUMAN ( 11  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|Q9NP59|S40A1_HUMAN ( 12  of  13 )
Getting the summarization for censored missing values per subplot for protein  sp|Q9UHI5|LAT2_HUMAN ( 13  of  13 )
MeenaChoi commented 6 years ago

I recommend to remove iRT protein before you start.

pdf file for profile plot is saved under your working directory.