[BioC] Combine function in matchprobes

[Robert Gentleman]

Well, the man page for combine says:
Usage:

     combine(batch, probepkg, newcdf, verbose=TRUE)

Arguments:

   batch: A 'list' of AffyBatches.

probepkg: A character vector of the same length as 'batch', containing
          the names of the probe sequences libraries (for example,
          'hgu133aprobe') that go with the AffyBatches.

  newcdf: Character. The name of the name CDF environment that is to
  be
          created.

 verbose: Logical. If TRUE, messages are printed to the console.


And I do not see where you have indicated the probe packages?
You do need them (and they are available on the Bioconductor site).

 Robert


On Fri, Jan 16, 2004 at 03:03:27PM -0500, Tan, MinHan wrote:
> Hi,
>  
> I tried combining 2 Affybatches (HGU133A and HGU133Plus 2.0) using
> combine in matchprobes, but ran into the following problems.
>  
> I used both R 1.9.0 and R 1.8.1 with the latest downloads from
> Bioconductor.
>  
> > merged.data <- combine(list(DataHGU133A,DataHGU133P), c("hgu133acdf",
> "hgu133plus2cdf"), "mycdf", verbose=TRUE)
> package:hgu133acdf      hgu133acdf      
> package:hgu133plus2cdf  hgu133plus2cdf  
> 0 probes in common between hgu133acdf and hgu133acdf 
> Error in sequs[[i]] : subscript out of bounds
>  
> Looking at the combine function, I seem to be running into problems at
> this point? 
> 
> > tmp <- get(upp[1], uppname[1])
> > str(tmp)
> length 0 <environment>
> > upp[1]
> [1] "hgu133acdf"
> > uppname[1]
> [1] "package:hgu133acdf"
> 
>  
> Your advice is very much appreciated!
>  
>  
> Min-Han Tan
> 
> This email message, including any attachments, is for the so...{{dropped}}
> 
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| Robert Gentleman                 phone : (617) 632-5250                   |
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