[BioC] Fwd: modifyWeights Problem

[James W. MacDonald]

stephen sefick wrote:
>>> 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

OK. Back to this statement. If your array contains 6400 genes, then why 
are you not wondering about the length of your controlStatus vector?

 From ?controlStatus I get that the output is supposed to be a character 
vector giving the type of each spot on the array. You have 6400 spots, 
so the output should be a character vector of length 6400 saying what 
each spot type is. Since each array is identical, there is no need to 
say more than once what a particular spot is.

So it would appear to me that there is something amiss with the call to 
controlStatus(), as it is giving back something unexpected. I would look 
at the input you are feeding to that function to see if it is what you 
expect it to be.

As to your question of what to do with the 'status' vector, why do 
anything with it? Can't it just hang around in your .GlobalEnv with 
everything else?

Best,

Jim



-- 
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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