Entering edit mode
davidl@unr.nevada.edu
▴
140
@davidlunrnevadaedu-1371
Last seen 10.2 years ago
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 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
