[BioC] Error in PLW package plw()

Martin Morgan mtmorgan at fhcrc.org
Thu Mar 26 04:04:59 CET 2009

Hi Dave --

I think your plw is out of date; on this page


plw is at 1.2.0. Try the instructions here


to 'Update installed Bioconductor packages'


davidl at unr.nevada.edu writes:

> Hello list,
>     I am giving "Probe Level locally moderated median-t" (PLW) a try
> because the ROC curves on the spike-ins looked promising on the paper
> introducing it
> (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2358895).
> First, I think that the function plw() is using a background
> subtraction function that has been removed from the affy package since
> plw() is giving me this message:
> plwFit<-plw(rawdata, design=design, contrast=contrast, epsilon=1e-05)
> Background correcting and normalizing.  Error: could not find function
> "bg.correct.rma2" Error in pm(bg.correct.rma2(x, bgtype = 2)) : error
> in evaluating the argument 'object' in selecting a method for function
> pm'
> Is there anything I could do about this (an easy way to make it call
> bg.correct.rma() instead)?  This is in R 2.8.1, plw_0.99.2, and affy
> 1.20.2.  Second, I currently have a dataset consisting of 4 affymetrix

... paste the output of sessionInfo(), it'll be more comprehensive,
accurate, and easy.


> mouse 4302 arrays, but 3 are controls and 1 is from a mutant.  Plans
> are to add 2 more mutant arrays later, but preliminary data is being
> requested for now.  I was wondering if anyone could weigh in on what
> they might consider the most accurate ([True negatives+True
> Positives]/total) method for deriving measures of differential
> expression on this platform given the lack of replicates in the second
> group.  What do you think about PLW (I'm not a seasoned statistician,
> so I probably missed some things when reading the PLW paper)?  Thank
> you very much in advance for any help given.  I really appreciate all
> the help I've received from this list.  Cheers,
> Dave
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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