[Bioc-devel] package test failing due to CSAW

Vivek Bhardwaj bh@rdw@j @end|ng |rom |e-|re|burg@mpg@de
Tue Jun 25 10:16:08 CEST 2019

Hi All

The check of my package is failing locally due to the error in 
"csaw::scaledAverage" function. Untill version 3.9, I used to pass a 
DGElist object to this function call as follows:

/dat.y <- csaw::asDGEList(data, assay = assay.data)//# create DGElist 
from SE object
//dat.y <- edgeR::estimateCommonDisp(dat.y)//# estimate dispersion

/data.ab <- csaw::scaledAverage(dat.y, scale = 1, prior.count = 1) # get 
scaled average

Now in version 3.10 I get the following error:

Error in (function (classes, fdef, mtable) :
   unable to find an inherited method for function ‘assay’ for signature 
‘"DGEList", "character"’

Is CSAW not accepting DGElist anymore? How shall I replace this function 
call here?



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