[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
The code below may help:
>#AffyBatch68 = vector of any u6800 arrays (one or more)
>#AffyBatch95 = vector of any 95av2 arrays (one or more)
>newcdf = "comb")
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
size of arrays=0x0 features (1078 kb)
cdf=comb (5217 affyids)
number of samples=2
number of genes=5217
Have fun customizing MSN Messenger learn how here!
More information about the Bioconductor