Open slzhao opened 4 months ago
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Hello,
Can someone help me to understand the QC process?
Based on this link: https://www.bioconductor.org/packages/release/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#4_QC__Pre-processing
It mentioned:
in fact in the code (NanoStringGeoMxSet-qc.R), it works as:
lowReads <- sData(object)["Raw"] < cutoff
This looks correct in code (fewer raw reads than cutoff was labeled) but incorrect in the document (more raw reads than cutoff was removed).Similarly (but reversely), the document mentioned:
But in the code, it works as:
This looks incorrect in code (fewer negative counts than cutoff was labeled) but correct in the document (more negative counts should be labeled).