Hello everyone. I am currently struggling with lc-ms processing of raw data (.mzML files) and looking over the OptiLCMS code i saw the different “EXCEPTION POINT CODES”. This codes serve as error handlers, but they are coded and they don’t show where the problem is or what is the problem. As they connect with the MessageOutput Error, is it possible to see the line of code that has made the error but not exactly why.
ERROR:upper value must be greater than lower value
Error in PerformROIExtraction(datapath = DataFiles, rt.idx = 0.9, rmConts = TRUE) :
EXCEPTION POINT CODE: RMS1
Execution halted
this example told me that my data don’t have the MSnExp class within the data and looking within the code there are some parts that work onDisk and other than work inMemory.
Whereas the other error comes in:
ERROR:upper value must be greater than lower value
Error in ImportRawMSData(path = DataFiles, metadata = c(“./metadata.txt”), :
EXCEPTION POINT CODE: RMS2
Execution halted
that tells me that raw_data can’t be “MSnExp” related.
Anyway i would like to know what are the meanings of the different exception point codes, just like two of them that already explain them:
“EXCEPTION POINT CODE: Peak Picking. Please adjust your parameters and try again.”
“EXCEPTION POINT CODE: Peak Alignment. Please adjust your parameters and try again”
I would like to know what these codes mean:
PO2
PU3
RMS1
RMS2
RT1
I am working following LCMSMS_Raw_Spectral_Processing.html in two different steps due to memory limitations: first Extract the ROIs and perform Parameters Optimization; and then importing the data with ImportRawMS, following by the Peak Profiling and the Annotations