[BioC] Error in PLW package plw()

davidl at unr.nevada.edu davidl at unr.nevada.edu
Thu Mar 26 03:44:21 CET 2009

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

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 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,


More information about the Bioconductor mailing list