[BioC] Fwd: modifyWeights Problem

[James W. MacDonald]

Hi Stephen,

First off, this isn't a forum, so 'bumping' your question by forwarding 
it again is more likely than not to backfire. Better to accept the fact 
that nobody cares to answer your question than incur wrath and decrease 
chances of further questions being answered, if people decide you are a 
less than model citizen.

Additionally, note that the maintainer of limma is Australian, so the 
likelihood of getting an answer from the most expert of us in the middle 
of his night is pretty small.

stephen sefick wrote:
> ---------- 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

As you note this isn't reproducible, which is probably reason #1 that 
your question has been ignored. I am positive you could have mocked up 
some code to show what the perceived problem is so prospective helpers 
might have something to look at.

> 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))

Three things.

1) Why are you stuffing this status vector into your RGList? There are 
expectations of the form for this object for downstream functions and 
having some extra cruft added may have unintended consequences.

2) The third argument for modifyWeights is supposed to be unique values 
of the second argument. From your code this doesn't appear to be the case.

3) What is dim(RG$weights)?

Best,

Jim


> 
> --
> 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
> 
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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