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
[Bioc-devel] package test failing due to CSAW
2 messages · Vivek Bhardwaj, Aaron Lun
This behavior has been deprecated since May 18 2018, looking at the Git logs here: https://github.com/LTLA/csaw/commits/master/R/scaledAverage.R 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. -A
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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