[BioC] matchprobes package:Is there a bug?

david neil hayes davidneilhayes at hotmail.com
Tue Dec 16 22:22:32 MET 2003

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:

>#AffyBatch68 = vector of any u6800 arrays (one or more)
>#AffyBatch95 = vector of any 95av2 arrays (one or more)
>Res <- 
>newcdf = "comb")
package:hugeneflprobe   hugeneflprobe
package:hgu95av2probe   hgu95av2probe
131541 probes in common between hugeneflprobe and hugeneflprobe
34456 probes in common between hugeneflprobe, hgu95av2probe and 
34428 unique probes in common
>comb <- Res$cdf
>NewSet <- Res$dat
AffyBatch object
size of arrays=0x0 features (1078 kb)
cdf=comb (5217 affyids)
number of samples=2
number of genes=5217
[1] "CL2001031606AA.CEL"
[1] "AD2.CEL"

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