[BioC] Fwd: modifyWeights Problem

[stephen sefick]

Let me start out by apologizing for posting twice.  I realized after
the fact that I had accidently subscribed to the developer forum, so I
then fowarded my message to the bioconductor list.  Which, I think, is
the appropriate place for this question.  Again, I am sorry.  The rest
of my response is in line below...

On Thu, Feb 4, 2010 at 2:11 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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.

I must have misread the users guide.  I will put it wherever it is
proper to do so.  In an object called status?

> 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.

I have tried many combinations - with both a subset and the entire
list neither works.  I got errors that said that the number of rows in
status does not match the weights that I would like to modify.  I have
six arrays with 6400 rows.

> 3) What is dim(RG$weights)?

 6400    6

I have never worked with microarray data before, so I am learning as I
go along.  I have a template for an analysis that I am trying to
recreate without help from the original person who did the analysis.
We have two different sets of "results" that are very different but
from the same contrasts.  So, We need to track down which one of the
results is correct... they have very different implications for the
biological significance of the results.

I didn't expect a response at 12:20 at night.  I just felt I needed to
get the question out before I went to bed for the express purpose of
folks that may help being all over the world.

Agian, I apologize for any inconvenience.


Thanks so much for all of the help.

Stephen

> 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
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>



-- 
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