[BioC] combineAffyBatch

[Kauer Maximilian Otto]

Dear list,

I am trying to merge to affybatches with combineAffyBatch from the matchprobes package. One is hgu133a (33 arrays), the other hgu133plus2 (12 arrays).

While the example in the vignette works fine, I tried to make the affybatches for my data so it is exactly as in the vignette but I always get an error like this:

Loading required package: hgu133aprobe
Loading required package: hgu133plus2probe
package:hgu133aprobe    hgu133aprobe    
package:hgu133plus2probe        hgu133plus2probe        
241837 unique probes in common
Error in combine(pDataX, pDataY) : data.frames contain conflicting data:
        non-conforming colname(s): fromFile

I would be grateful for any suggestions or if anybody knows another good way to combine the data.

Thanks!
Max

Here's my code:

h133a <- list.celfiles()
h133plus2 <- list.celfiles()
pd1 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(h133plus2),row.names = paste("f", seq(1:12), sep="")))
pd2 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(h133a),row.names = paste("f", seq(1:33), sep="")))
h133a.ab <- read.affybatch(filenames = h133a, phenoData = pd2)
h133plu2.ab <- read.affybatch(filenames = h133plus2, phenoData = pd1)
res <- combineAffyBatch(list(h133a.ab, h133plu2.ab), c("hgu133aprobe", "hgu133plus2probe"), newcdf="hgu133comb", verbose=TRUE)

> sessionInfo()
R version 2.5.0 (2007-04-23) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "tools"     "tcltk"     "stats"     "graphics"  "grDevices" "utils"    
[7] "datasets"  "methods"   "base"     

other attached packages:
hgu133plus2probe     hgu133aprobe      matchprobes             affy           affyio 
        "1.16.0"         "1.16.0"          "1.8.1"         "1.14.1"          "1.4.0" 
         Biobase            svGUI          svViews             svIO           svMisc 
        "1.14.0"          "0.9-5"          "0.9-5"          "0.9-5"          "0.9-5" 
          R2HTML 
          "1.58"