Hello,

I am running R to combine data from three Affy platforms using the following libraries (Affy, hgu133a2.db, and hgu133plus2.db).  After loading the libraries and reading in the data, I run the following to output a combined dataset with the common probes on all three Affy platforms but get an error message:

...................
comdata2 <- combineAffyBatch(list(data1, data2, data3), probepkg=c("hthgu133aprobe", "hgu133a2probe", "hgu133plus2probe"), newcdf="comhgu133")
package:hthgu133aprobe  hthgu133aprobe
package:hgu133a2probe   hgu133a2probe
package:hgu133plus2probe        hgu133plus2probe
241661 unique probes in common

Error in as.vector(x, "character") :
  cannot coerce type 'closure' to vector of type 'character'
....................


If I run the code with only two datsets (data1 and data 2 or data 1 and data 3, it runs fine:  e.g.: comdata2 <- combineAffyBatch(list(data1, data2), probepkg=c("hthgu133aprobe", "hgu133a2probe"), newcdf="comhgu133")).  The problem seems to occur with combining all three datasets.  Does anyone know how to fix this?

Thanks!
Anu



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