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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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QC questions #196

Open slzhao opened 4 months ago

slzhao commented 4 months ago

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:

Raw sequencing reads: segments with >1000 raw reads are removed.

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:

segments with low negative counts (1-10) are not necessarily removed

But in the code, it works as:

    lowNegs <- 
        data.frame("LowNegatives"=apply(negativeGeoMeans < cutoff, 1, sum) > 0)

This looks incorrect in code (fewer negative counts than cutoff was labeled) but correct in the document (more negative counts should be labeled).

github-actions[bot] commented 4 months ago

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