[BioC] matchprobes package:Is there a bug?

[w.huber at dkfz-heidelberg.de]

Hi David,

it looks like the newly created synthesized AffyBatch does not contain all
the necessary slots and dimnames. I'll have a look into that as soon as
possible. In the meanwhile you should be able to work around this
by setting the gene- and samplenames manually.

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 Tue, 16 Dec 2003, david neil hayes wrote:

> To those who have not yet seen the matchprobes package, it is worth a look
> and I thank Dr. Gentleman and Dr. Huber for this addition to Bioconductor.
>
> I have the following problem with the "combine" function, however, and I
> wonder if it is a bug.
>
> I am able to generate the new "combined" affybatch object as expected,
> however there are problems with the gene and sample names.
>
> geneNames(AffyBatch) returns a list of names from the new "combined" object,
> however when I extract the expression matrix from the AffyBatch object(using
> exprs(AffyBatch)), the matrix has no gene or sample names associated with it
> (no row or column names.
>
> sampleNames(AffyBatch) returns a character vector of length 0
>
> Any thoughts?
>
> The code below may help:
>
> >library(affy)
> >library(matchprobes)
> >
> >#AffyBatch68 = vector of any u6800 arrays (one or more)
> >#AffyBatch95 = vector of any 95av2 arrays (one or more)
> >
> >Res <-
> >combine(list(AffyBatch68,AffyBatch95),c("hugeneflprobe","hgu95av2probe"),
> >newcdf = "comb")
> package:hugeneflprobe   hugeneflprobe
> package:hgu95av2probe   hgu95av2probe
> 131541 probes in common between hugeneflprobe and hugeneflprobe
> 34456 probes in common between hugeneflprobe, hgu95av2probe and
> hugeneflprobe
> 34428 unique probes in common
> >
> >comb <- Res$cdf
> >NewSet <- Res$dat
> >NewSet
> AffyBatch object
> size of arrays=0x0 features (1078 kb)
> cdf=comb (5217 affyids)
> number of samples=2
> number of genes=5217
> annotation=
> >sampleNames(NewSet)
> character(0)
> >sampleNames(AffyBatch95)
> [1] "CL2001031606AA.CEL"
> >sampleNames(AffyBatch68)
> [1] "AD2.CEL"
>
> _________________________________________________________________
> Have fun customizing MSN Messenger — learn how here!
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>