[BioC] Fwd: modifyWeights Problem

[stephen sefick]

---------- Forwarded message ----------
From: stephen sefick <ssefick at gmail.com>
Date: Wed, Feb 3, 2010 at 11:31 PM
Subject: modifyWeights Problem
To: bioc-devel at stat.math.ethz.ch


I am using the limma packages for the first time, and I need help with
the modifyWeights function.  I have about three years of experience
with R programing, but this is the first time that I have run an
analysis with a bioconductor package.  I have included the code below.
 I know that this is not a reproducible example and I would gladly
give any more information requested.  I am trying to modify the
weights of genes that I know are housekeeping genes (upweight).  I can
not get the modifyWeights function to work to save my life.  The
weights array is 6400, 6.  The control status vector is 12800- that
seems like only two of the arrays are being represented???????  I
don't know what is wrong.  Any help would be greatly appreciated
thanks,

Stephen Sefick

library(limma)
library(marray)
library(convert)
library(statmod)
#read in targets file
targets <- readTargets("targets.txt", row.names="Name")
#weight everything with flags !cutoff=0!
RG <- read.maimages(targets$FileName, source="genepix",
wt.fun=wtflags(cutoff=-50 weight=0))
#read .gal file
#remove extra tab in file

a <- readGAL()
b <- a[,-6]
RG$genes<-b
#spot types file
spottypes <- readSpotTypes()
RG$genes$Status <- controlStatus(spottypes, RG$genes)

##################CHANGE weighting for spot types#####################
######################################################################
multiply <- c(1,0,2,0,1,0,1,1,1)
######################################################################
######################################################################

a <- unique(RG$genes$ID)
status=RG$genes$Status
w <- modifyWeights(RG$weights, RG$genes$Status, a, c(0, 1))

--
Stephen Sefick

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

                                                               -K. Mullis



-- 
Stephen Sefick

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

								-K. Mullis