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hansenlab / minfi

Devel repository for minfi
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getBeta of RGChannelSet #82

Closed Rory-R-Wilson closed 7 years ago

Rory-R-Wilson commented 7 years ago

Dear developers,

It seems that the options of "offset" and "type" do not work when applying getBeta() directly to an RGChannelSet. No warning or error message is given, the betas are simply returned as calculated with no offset. I am not sure if this is intentional or not - I could not directly determine this from the documentation. I just wanted to bring it to your attention.

Thank you,

Rory

Jfortin1 commented 7 years ago

Hi Rory,

Thanks for letting us know. Indeed the function for RGChannelSet should be

setMethod("getBeta", signature(object = "RGChannelSet"), function(object, ...) { object <- preprocessRaw(object) callGeneric(object, ...) })

instead of

setMethod("getBeta", signature(object = "RGChannelSet"), function(object, ...) { object <- preprocessRaw(object) callGeneric(object) })

Going to fix that. Thanks!

Rory-R-Wilson commented 7 years ago

Okay! Thanks for your quick feedback. Rory

On Sun, Oct 30, 2016 at 5:01 PM, Jean-Philippe Fortin < notifications@github.com> wrote:

Hi Rory,

Thanks for letting us know. Indeed the function for RGChannelSet should be

setMethod("getBeta", signature(object = "RGChannelSet"), function(object, ...) { object <- preprocessRaw(object) callGeneric(object, ...) })

instead of

setMethod("getBeta", signature(object = "RGChannelSet"), function(object, ...) { object <- preprocessRaw(object) callGeneric(object) })

Going to fix that. Thanks!

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