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Nanostring-Biostats / GeomxTools

Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.
MIT License
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bug in setSegmentQCFlags() minArea filtering #171

Closed fnew closed 1 year ago

fnew commented 2 years ago

When below code is run on protein data, segments with area greater than 20 are flagged as failing QC because of low area. GeomxTools v3.0.1

 proteinData <- setSegmentQCFlags(proteinData, qcCutoffs = list(percentSaturation = 45,
                                                               minSegmentReads=1000, 
                                                               percentAligned=80, 
                                                               minNegativeCount=10, 
                                                               maxNTCCount=60, 
                                                               minNuclei=16000, 
                                                               minArea=20))

SPG_protein_data.zip

NicoleEO commented 1 year ago

@maddygriz can we close this bug?

maddygriz commented 1 year ago

yep, closing