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

Hi Paul, please see the answers below. On Fri, 12 Feb 2010 16:03:13 +0000, Paul Geeleher wrote > 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) Looking at the function call, indeed there is the argument 'modColumn=' twice. For once, the R error message really indicated the source of the problem. > 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 Well, if you remove that, there still is the argument 'modColumn="Antibody"'. Do you have a column called 'Antibody' in your pData of X? If not, then that's the reason for this error. I admit that I probably need to add a check to see if the value for 'modColumn' actually exists before returning such an error. If there is a column called 'Antibody' in pData (X), then something strange is going on here and I would need more information to look into this, starting with the output of sessionInfo(). Regards, Joern --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246927