problem with combineAffyBatch
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@jared-j-bisogni-1284
Last seen 9.6 years ago
Hello, I have been trying to combine data from rgu34a and rtu34 chips using ?combineAffyBatch? from the package matchprobes. My problem is that the resulting AffyBatch object has array sizes of 0x0. I am running version 2.1.0 of R for windows and have version 1.0.22 of matchprobes. Here is my code: pd1<-new("phenoData",pData=data.frame(id="ny"), varLabels=list("phenovar")) pd2<-new("phenoData",pData=data.frame(id="ge"), varLabels=list("phenovar")) > x1<-read.affybatch(file1,compress=TRUE, phenoData=pd1) > x2<-read.affybatch(file2,compress=TRUE, phenoData=pd2) comb<-combineAffyBatch(list(x1,x2),c("rgu34aprobe","rtu34probe"), "newset",verbose=TRUE) package:rgu34aprobe rgu34aprobe package:rtu34probe rtu34probe 16612 unique probes in common Here is what I get >comb $dat AffyBatch object size of arrays=0x0 features (523 kb) cdf=newset (1036 affyids) number of samples=2 number of genes=1036 annotation= $cdf <environment: 074edc14=""> What can I do to fix this? Jared
rgu34a rtu34 matchprobes rgu34a rtu34 matchprobes • 866 views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Hi Jared, since the "combined" array is not really a physical array with x- and y-dimensions, the size information is meaningless. Does the data rom the 1036 probe sets you get make sense? Best wishes Wolfgang Jared J. Bisogni wrote: > Hello, > I have been trying to combine data from rgu34a and rtu34 chips using > ?combineAffyBatch? from the package matchprobes. My problem is that the > resulting AffyBatch object has array sizes of 0x0. I am running version > 2.1.0 of R for windows and have version 1.0.22 of matchprobes. > > Here is my code: > > > pd1<-new("phenoData",pData=data.frame(id="ny"), varLabels=list("phenovar")) > pd2<-new("phenoData",pData=data.frame(id="ge"), varLabels=list("phenovar")) > > >>x1<-read.affybatch(file1,compress=TRUE, phenoData=pd1) >>x2<-read.affybatch(file2,compress=TRUE, phenoData=pd2) > > > comb<-combineAffyBatch(list(x1,x2),c("rgu34aprobe","rtu34probe"), > "newset",verbose=TRUE) > > package:rgu34aprobe rgu34aprobe > package:rtu34probe rtu34probe > 16612 unique probes in common > > Here is what I get > > >>comb > > $dat > AffyBatch object > size of arrays=0x0 features (523 kb) > cdf=newset (1036 affyids) > number of samples=2 > number of genes=1036 > annotation= > > $cdf > <environment: 074edc14=""> > > What can I do to fix this? > Jared > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber
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