Question: matchprobes package:Is there a bug?
13.8 years ago by
david neil hayes • 70
david neil hayes • 70 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","hgu95av2prob e"), >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)  "CL2001031606AA.CEL" >sampleNames(AffyBatch68)  "AD2.CEL" _________________________________________________________________ Have fun customizing MSN Messenger learn how here!
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