[BioC] Using combineReplicates in computeRunningMedians() function in Ringo

[Paul Geeleher]

Hi list,

I'm trying to use computeRunningMedians() to combine my replicate
arrays using the modColumn and combineReplicates arguements. My code
looks something like this:

pData(X)$Cy5 <- targets$Cy5
smoothComb <- computeRunningMedians(X, modColumn="Antibody",
winHalfSize=400, min.probes=3, probeAnno=pA, modColumn="Cy5",
combineReplicates=TRUE)

Basically I'm attaching my column of interest to pData of X and
running the smoothing. It however give me this error:

Error in computeRunningMedians(X, modColumn = "Antibody", winHalfSize = 400,  :
  formal argument "modColumn" matched by multiple actual arguments

or if I remove "modColumn='Cy5'" it gives this error:

Chromosome 10 ...
 ... Error: subscript out of bounds

I think I'm doing something wrong in attaching Cy5 to phenoData of X,
I'm wondering if anyone has any ideas what I could do?

Paul

-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com