[BioC] modifyWeights Problem

[stephen sefick]

There are housekeeping genes that should not be differentially
expressed.  I was trying to up weight these in the normalization
process.  Also, I am sorry if I am a bother, but what I am trying to
recreate in the normalization process is this:

background normalization
two dimensional normalization for spatial and then print tip loess
scale normalization between arrays

#MA <- maNormMain(as(RG, "marrayRaw"),  f.loc = list(maNorm2D(weights=w)))
MA <- maNorm(as(RG, "marrayRaw"), norm="twoD")
MA <- normalizeWithinArrays(as(MA, "MAList"))
##################################################################

#MA <- normalizeWithinArrays(RG)

#scale normalization between arrays
WA <- normalizeBetweenArrays(as(MA, "MAList"), method="scale")

I appreciate everyone's help.  I will work on this tomorrow, and try
to form my questions more coherently.


thanks,

Stephen

On Thu, Feb 4, 2010 at 4:51 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>
>> Date: Wed, 3 Feb 2010 23:31:40 -0600
>> From: stephen sefick <ssefick at gmail.com>
>> To: bioc-devel at stat.math.ethz.ch
>> Subject: [Bioc-devel] modifyWeights Problem
>> Content-Type: text/plain; charset=UTF-8
>>
>> 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$FileName, source="genepix",
>> wt.fun=wtflags(cutoff=-50 weight=0))
>> #read .gal file
>> #remove extra tab in file
>>
>> a <- readGAL()
>
> It is highly unlikely that you need to read a GAL file.  The limma User's
> Guide tells you that you only need to do this with SPOT input, not with
> GenePix.
>
> It is obvious from the information you give that whatever GAL file you are
> reading, it doesn't match your GenePix files, because it has twice as many
> rows.
>
>> b <- a[,-6]
>> RG$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))
>
> Have you looked at the help page for modifyWeights?  I'd think a quick read
> would tell you that your input arguments aren't the right dimensions, so
> there's no chance of this call working correctly.
>
> I also wonder what you're trying to achieve with modifyWeights, and whether
> you need it at all?  This function is only needed for special situations.
>
> Best wishes
> Gordon
>
>> --
>> Stephen Sefick
>
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