oligoDefunct: Defunct Functions in Package 'oligo'
In benilton/oligoOld: Preprocessing tools for oligonucleotide arrays

The functions or variables listed here are no longer part of 'oligo'

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fitPLM(...)
coefs(...)
resids(...)

...

Arguments.

fitPLM was replaced by fitProbeLevelModel, allowing faster execution and providing more specific models. fitPLM was based in the code written by Ben Bolstad in the affyPLM package. However, all the model-fitting functions are now in the package preprocessCore, on which fitProbeLevelModel depends.

coefs and resids, like fitPLM, were inherited from the affyPLM package. They were replaced respectively by coef and residuals, because this is how these statistics are called everywhere else in R.