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Review vignette from link below.
https://github.com/Nanostring-Biostats/DSPPlugins/blob/master/DSPPlugVolcanoPlot/LabeledVolcanoPlot-plugin-vignette.docx
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Add metrics calculated in qc to the protocolData
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Optional parameter to add 1 across the board to all your counts (this should be on by default to match DA). All geomean or log functions need to check if this was done to not add more of an offset to …
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- [x] Match default cutoffs in DA
- [x] Change AOI QC to explicitly say seq QC
- [x] Minimize QC groupings to only the defaults in DA
- [x] Make sure values are taken as numeric
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- [x] NTC samples should be removed from the sample list
- [x] The NTC sample count should be appended to protocolData to corresponding sample on the same plate in the same section (NTC with same pla…
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I am having a hard time getting GeomxTools working on a fresh install of R 4.1.0
Here is the error I just encountered.
```
Error: Failed to install 'GeomxTools' from GitHub:
System command 'Rc…
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@rvitancol we seem to be having some mishmash of default column naming.
Sample names are referred to as SampleID or Sample_ID (DA doesn't have a consistent name for this column since it is a mix of …
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target_demoData = normalize(target_demoData , data_type="RNA", norm_method="quant", desiredQuantile = .9, toElt = "q_norm")
Why do you suggest desiredQuantile = .9 ? I know GeoMx recommends to use …
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/calebclass/NanoTube
Confirm the following by edit…