Bug/typo with normalization calculations in NanoStringRccSet-normalize.R

[nranthony]

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)

NanoStringNCTools/R/NanoStringRccSet-normalize.R

Line 13 in e1504e2

pcG <- summary(object, 2L, elt = toElt)[, "GeomMean"]

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]

Hi @nranthony,

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

Thanks,
Nicole

@maddygriz heads up