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
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