[BioC] Combine function in matchprobes

[w.huber at dkfz-heidelberg.de]

Hi Min-Han Tan,

You specified CDF packages instead of probe packages.  The combine
function will produce a more intelligible error message rather than the
one you reported in version 1.0.3 which will be on the web shortly.

Best wishes
 Wolfgang

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber
-------------------------------------

On Fri, 16 Jan 2004, Robert Gentleman wrote:

> 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}}
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
> --
> +---------------------------------------------------------------------------+
> | Robert Gentleman                 phone : (617) 632-5250                   |
> | Associate Professor              fax:   (617)  632-2444                   |
> | Department of Biostatistics      office: M1B20                            |
> | Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
> +---------------------------------------------------------------------------+
>
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