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Nanostring-Biostats / NanoStringNCTools

Tools for NanoString Technologies nCounter Technology for reading RCC files into an ExpressionSet derived object, QC and normalization.
MIT License
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Bug/typo with normalization calculations in NanoStringRccSet-normalize.R #28

Closed nranthony closed 1 year ago

nranthony commented 2 years ago

Normalization values do not match those calculated using nSolver.

I suspect that object on line 13 should be posCtrl from the line above:

posCtrl <- positiveControlSubset(object) https://github.com/Nanostring-Biostats/NanoStringNCTools/blob/e1504e2c25463dff6f55b7c2f236867119e55889/R/NanoStringRccSet-normalize.R#L13

If I change object on line 13 to be posCtrl the Content Normalization Factors and resulting normalized counts match that of nSolver. As it stands the positive control normalization factors are calculated from the entire gene set passed using object.

NicoleEO commented 2 years ago

Hi @nranthony,

Thanks for using NanoStringNCTools. If you like, feel free to fork and submit a PR to correct.

Thanks, Nicole

@maddygriz heads up