readMSData error

August 20, 2020, 03:57:37 PM

Anyone know where/why this error occurs when reading an mzXML file that was converted from SciEx wiff using their Converter tool? See below. Thanks.

> raw_data <- readMSData(files = mzXML, pdata = new("NAnnotatedDataFrame", pd),
+ mode = "onDisk")
Error: Can not open file /Users/errontitus/lab-private/tox-mass-spec/data/2020-08-18-test-dataset/blood/QTOF_CDS_2020_08_18_CT46860A UCLM BLOOD 2150_19.mzXML! Original error was: Error in pwizModule$open(filename): [References::resolve()] Failed to resolve reference.
object type: N4pwiz6msdata23InstrumentConfigurationE
reference id: instrumentConfiguration19
referent list: 1
instrumentConfiguration1

Re: readMSData error

Reply #1 – August 20, 2020, 05:47:06 PM

Update: this problem went away after I switched to using proteowizard for my wiff -> mzXML conversion.