[BioC] combineAffyBatch

[Martin Morgan]

Hi Max --

For data.frames, combine makes sure that any cell shared between two
data frames (i.e., cells with the same row and column names in each
data frame) have the same data. In your example, an example of a
shared cell would be pd1["f1", "fromFile"] and pd2["f1",
"fromFile"]. Presumable the contents of these cells is different, so
there is no sensible way to combine them.

A simple solution might be to rename the rows:

> pd1 <- data.frame(fromFile = I(LETTERS[1:5]),
+                   row.names = paste("f", seq(1:5)))
> pd2 <- data.frame(fromFile = I(letters[1:5]),
+                   row.names = paste("g", seq(1:5)))
> res <- combine(pd1, pd2)

Martin

"Kauer Maximilian Otto" <maximilian.kauer at ccri.at> writes:

> 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"
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org