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Question: matchprobes package:Is there a bug?
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gravatar for david neil hayes
13.6 years ago by
david neil hayes70 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) [1] "CL2001031606AA.CEL" >sampleNames(AffyBatch68) [1] "AD2.CEL" _________________________________________________________________ Have fun customizing MSN Messenger — learn how here!
ADD COMMENTlink modified 13.6 years ago by Wolfgang Huber13k • written 13.6 years ago by david neil hayes70
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gravatar for Wolfgang Huber
13.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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","hgu95av2pr obe"), > >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@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 13.6 years ago by Wolfgang Huber13k
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gravatar for Wolfgang Huber
13.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear David, On Tue, 16 Dec 2003, david neil hayes wrote: > 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. I have just checked in a revised version of combine that does produce the sampleNames of the combined object. These are the column names of the exprs slot. There are no rowNames, as usual for AffyBatches (if anything they would be probeNames). These updates should be available from the "Developmental Packages" section of the website soon (check for matchprobes version 1.0.2). 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
ADD COMMENTlink written 13.6 years ago by Wolfgang Huber13k
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