Using qsmooth in the generic Affymetrix processing pipeline

[axitamm]

Thank you for this amazing package (and quantro)!

I would like to obtain your best thoughts about integrating qsmooth into the generic Affymetrix rma processing pipeline. By generic, I mean the following:

library(affy)

#read the .cel files in the working directory
expdata<-ReadAffy()

#the generic "rma" processing (which as you know can also be achieved by using the function affy::rma instead of affy::expresso)
eset <- expresso(expdata, bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")

How do you suggest smooth quantile normalization be incorporated in the code above?

Thank you!

[stephaniehicks]

Hi @axitamm,

Could you post your comment on the Bioconductor Support site (https://support.bioconductor.org)? I will answer any problems about the package itself here, but prefer to answer the types of questions you are asking on the support site.

Thanks
Stephanie

[stephaniehicks]

Closing this issue too.