[Bioc-devel] package test failing due to CSAW

Aaron Lun |n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Wed Jun 26 08:12:16 CEST 2019

This behavior has been deprecated since May 18 2018, looking at the Git 
logs here:


I eventually got around to removing it last month, so the deprecation 
warning would have existed for 2 release cycles. That's fair game to me.

The reason for this is that filtering in the csaw workflow is usually 
done before conversion to a DGEList, so it makes more sense to apply 
scaledAverage() on SE objects. In fact, you're *meant* to run it on SE 
objects, hence the deprecation of the DGEList inputs

In your case, you have scale=1 so you might as well just call 
edgeR::aveLogCPM() directly. scaledAverage() just mimics this function 
with some careful scaling of the prior count when scale!=1.


On 6/25/19 1:16 AM, Vivek Bhardwaj wrote:
> 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?
> Thanks,
> Vivek
> 	[[alternative HTML version deleted]]
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