Concatenating or merging two or more ExpressionSet objects
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@richard-leduc-4611
Last seen 7.2 years ago
Hello All, I am somewhat new to R and definitely new to Bioconductor, so the answer to this may be painfully obvious, but I have failed to find it. We have a data processing pipeline that creates and analyzes microarray data with Bioconductor (no surprise there). The pipeline creates ExpressionSet objects that are written to the file system in RData files. I have been asked to write a block of code that (amongst other things) loads two (or more) ExpressionSets from different RData files, checks that they have same row names (to validate that they are from the same type of array), and concatenate them into one larger expression set. I can get everything up to the last step. Is there a simple way to merge two ExpressionSet objects? Thanks, Rich -- Richard LeDuc Associate Scientist/Bioinformaticist Great Lakes Bioenergy Research Center University of Wisconsin - Madison (608) 890-0007
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@christos-hatzis-2616
Last seen 7.2 years ago
See 'combine' method for eSets: combine(eSet,eSet): Combine two eSet objects. To be combined, eSets must have identical numbers of featureNames, distinct sampleNames, and identical annotation -Christos -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Richard Leduc Sent: Monday, April 25, 2011 2:59 PM To: bioconductor at r-project.org Subject: [BioC] Concatenating or merging two or more ExpressionSet objects Hello All, I am somewhat new to R and definitely new to Bioconductor, so the answer to this may be painfully obvious, but I have failed to find it. We have a data processing pipeline that creates and analyzes microarray data with Bioconductor (no surprise there). The pipeline creates ExpressionSet objects that are written to the file system in RData files. I have been asked to write a block of code that (amongst other things) loads two (or more) ExpressionSets from different RData files, checks that they have same row names (to validate that they are from the same type of array), and concatenate them into one larger expression set. I can get everything up to the last step. Is there a simple way to merge two ExpressionSet objects? Thanks, Rich -- Richard LeDuc Associate Scientist/Bioinformaticist Great Lakes Bioenergy Research Center University of Wisconsin - Madison (608) 890-0007 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@vincent-j-carey-jr-4
Last seen 6 weeks ago
United States
in principle, the combine method will do it. to read about it, use ?"combine,eSet,eSet-method" On Mon, Apr 25, 2011 at 2:59 PM, Richard Leduc <rleduc at="" glbrc.wisc.edu=""> wrote: > Hello All, > > I am somewhat new to R and definitely new to Bioconductor, > so the answer to this may be painfully obvious, but I have failed to find it. > > We have a data processing pipeline that creates and analyzes > microarray data with Bioconductor (no surprise there). The pipeline creates > ExpressionSet objects that are written to the file system in RData files. > > I have been asked to write a block of code that (amongst > other things) loads two (or more) ExpressionSets from different RData files, checks > that they have same row names (to validate that they are from the same type of > array), and concatenate them into one larger expression set. I can get > everything up to the last step. Is there a simple way to merge two ExpressionSet > objects? > > Thanks, > > Rich > -- > Richard LeDuc > Associate Scientist/Bioinformaticist > Great Lakes Bioenergy Research Center > University of Wisconsin - Madison > (608) 890-0007 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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