[BioC] Error in PLW package plw()

[Martin Morgan]

Hi Dave --

I think your plw is out of date; on this page

http://bioconductor.org/packages/2.3/bioc/html/plw.html

plw is at 1.2.0. Try the instructions here

http://bioconductor.org/docs/install/

to 'Update installed Bioconductor packages'

and...

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.

Martin

> 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
>
> _______________________________________________ Bioconductor mailing
> list Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
> archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793