combining/merging several ExpressionSet objects from SCAN
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Juliet Hannah ▴ 360
@juliet-hannah-4531
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All, SCAN outputs an ExpressionSet object for each CEL file. What is a nicer way to put them all into a matrix other than converting each one to a vector and then cbinding after each conversion? Thanks, Juliet [[alternative HTML version deleted]]
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@ryan-c-thompson-5618
Last seen 9 weeks ago
Icahn School of Medicine at Mount Sinai…
celfiles <- list.files(pattern=".*\\.CEL$") scan.esets <- lapply(celfiles, SCAN) scan.eset <- Reduce(combine, scan.esets) I forget what package the "combine" function is from, but I assume it's the same package that provides the ExpressionSet class. On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: > All, > > SCAN outputs an ExpressionSet object for each CEL file. What is a nicer way > to put them all into a matrix other than converting each one to a vector > and then cbinding after each conversion? > > Thanks, > > Juliet > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thanks Ryan. I'll try this out. What if the esets are already generated. So I have a bunch laying around. I'll look into your answer more and see if I can apply it to this situation. On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct@thompsonclan.org>wrote: > celfiles <- list.files(pattern=".*\\.CEL$"**) > scan.esets <- lapply(celfiles, SCAN) > scan.eset <- Reduce(combine, scan.esets) > > I forget what package the "combine" function is from, but I assume it's > the same package that provides the ExpressionSet class. > > > > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: > >> All, >> >> SCAN outputs an ExpressionSet object for each CEL file. What is a nicer >> way >> to put them all into a matrix other than converting each one to a vector >> and then cbinding after each conversion? >> >> Thanks, >> >> Juliet >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > [[alternative HTML version deleted]]
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qux <- combine(foo, bar, baz) if foo, bar, and baz are all ExpressionSets (or other eSets of suitable mien) with the same fData rows and pData columns. I did this the other day for a huge GEO dataset that came as 3 separate Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of course) On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah@gmail.com>wrote: > Thanks Ryan. I'll try this out. What if the esets are already generated. So > I have a bunch laying > around. I'll look into your answer more and see if I can apply it to this > situation. > > > On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct@thompsonclan.org> >wrote: > > > celfiles <- list.files(pattern=".*\\.CEL$"**) > > scan.esets <- lapply(celfiles, SCAN) > > scan.eset <- Reduce(combine, scan.esets) > > > > I forget what package the "combine" function is from, but I assume it's > > the same package that provides the ExpressionSet class. > > > > > > > > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: > > > >> All, > >> > >> SCAN outputs an ExpressionSet object for each CEL file. What is a nicer > >> way > >> to put them all into a matrix other than converting each one to a vector > >> and then cbinding after each conversion? > >> > >> Thanks, > >> > >> Juliet > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________**_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch/mailman/listinfo/bioconductor> > >> Search the archives: http://news.gmane.org/gmane.** > >> science.biology.informatics.**conductor< > http://news.gmane.org/gmane.science.biology.informatics.conductor> > >> > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* * * Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> [[alternative HTML version deleted]]
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Thanks Tim. I'm trying this out and looks like I did not think this through. So let's say I have several CEL files. I am spreading this out over a cluster. So I have myFiles = ("cel1.CEL","cel2,CEL") # pick one file fileToNormalize = myFiles[fileIndex] # normalize this to create eset normalized = SCAN(fileToNormalize) # create unique output name to save outFileName <- paste(fileToNormalize,".Rdata",sep="") save(normalized,file=outFileName) My problem is now an R one, but related to this problem. "normalized" must be given a unique name so that when I load all the esets back in they have different names. Any suggestions? On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > qux <- combine(foo, bar, baz) > > if foo, bar, and baz are all ExpressionSets (or other eSets of suitable > mien) with the same fData rows and pData columns. > > I did this the other day for a huge GEO dataset that came as 3 separate > Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of > course) > > > > On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah@gmail.com>wrote: > >> Thanks Ryan. I'll try this out. What if the esets are already generated. >> So >> I have a bunch laying >> around. I'll look into your answer more and see if I can apply it to this >> situation. >> >> >> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct@thompsonclan.org>> >wrote: >> >> > celfiles <- list.files(pattern=".*\\.CEL$"**) >> >> > scan.esets <- lapply(celfiles, SCAN) >> > scan.eset <- Reduce(combine, scan.esets) >> > >> > I forget what package the "combine" function is from, but I assume it's >> > the same package that provides the ExpressionSet class. >> > >> > >> > >> > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: >> > >> >> All, >> >> >> >> SCAN outputs an ExpressionSet object for each CEL file. What is a nicer >> >> way >> >> to put them all into a matrix other than converting each one to a >> vector >> >> and then cbinding after each conversion? >> >> >> >> Thanks, >> >> >> >> Juliet >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> ______________________________**_________________ >> >> Bioconductor mailing list >> >> Bioconductor@r-project.org >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >> https://stat.ethz.ch/mailman/listinfo/bioconductor> >> >> Search the archives: http://news.gmane.org/gmane.** >> >> science.biology.informatics.**conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >> >> >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > *He that would live in peace and at ease, * > *Must not speak all he knows, nor judge all he sees.* > * > * > Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> > [[alternative HTML version deleted]]
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use saveRDS(foo, file='foo.rds') and then when you reload it with readRDS, the resulting object can have whatever name you like. On Fri, Aug 9, 2013 at 12:47 PM, Juliet Hannah <juliet.hannah@gmail.com>wrote: > Thanks Tim. > > I'm trying this out and looks like I did not think this through. So let's > say I have several CEL files. > > I am spreading this out over a cluster. So I have > > myFiles = ("cel1.CEL","cel2,CEL") > > # pick one file > > fileToNormalize = myFiles[fileIndex] > > # normalize this to create eset > > normalized = SCAN(fileToNormalize) > > # create unique output name to save > > outFileName <- paste(fileToNormalize,".Rdata",sep="") > > save(normalized,file=outFileName) > > My problem is now an R one, but related to this problem. "normalized" must > be given a unique name so that when I load > all the esets back in they have different names. > > Any suggestions? > > > > > On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > >> qux <- combine(foo, bar, baz) >> >> if foo, bar, and baz are all ExpressionSets (or other eSets of suitable >> mien) with the same fData rows and pData columns. >> >> I did this the other day for a huge GEO dataset that came as 3 separate >> Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of >> course) >> >> >> >> On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah@gmail.com>wrote: >> >>> Thanks Ryan. I'll try this out. What if the esets are already generated. >>> So >>> I have a bunch laying >>> around. I'll look into your answer more and see if I can apply it to this >>> situation. >>> >>> >>> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct@thompsonclan.org>>> >wrote: >>> >>> > celfiles <- list.files(pattern=".*\\.CEL$"**) >>> >>> > scan.esets <- lapply(celfiles, SCAN) >>> > scan.eset <- Reduce(combine, scan.esets) >>> > >>> > I forget what package the "combine" function is from, but I assume it's >>> > the same package that provides the ExpressionSet class. >>> > >>> > >>> > >>> > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: >>> > >>> >> All, >>> >> >>> >> SCAN outputs an ExpressionSet object for each CEL file. What is a >>> nicer >>> >> way >>> >> to put them all into a matrix other than converting each one to a >>> vector >>> >> and then cbinding after each conversion? >>> >> >>> >> Thanks, >>> >> >>> >> Juliet >>> >> >>> >> [[alternative HTML version deleted]] >>> >> >>> >> ______________________________**_________________ >>> >> Bioconductor mailing list >>> >> Bioconductor@r-project.org >>> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >>> https://stat.ethz.ch/mailman/listinfo/bioconductor> >>> >> Search the archives: http://news.gmane.org/gmane.** >>> >> science.biology.informatics.**conductor< >>> http://news.gmane.org/gmane.science.biology.informatics.conductor> >>> >>> >> >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> >> -- >> *He that would live in peace and at ease, * >> *Must not speak all he knows, nor judge all he sees.* >> * >> * >> Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> >> > > -- *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* * * Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> [[alternative HTML version deleted]]
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Tim: I thought combine() has binary. Juliet: this often comes up. You can do assign("NAME", object) which is essentially equivalent to NAME <- object Then you can also get the object by get("NAME") Kasper On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah <juliet.hannah@gmail.com>wrote: > Thanks Tim. > > I'm trying this out and looks like I did not think this through. So let's > say I have several CEL files. > > I am spreading this out over a cluster. So I have > > myFiles = ("cel1.CEL","cel2,CEL") > > # pick one file > > fileToNormalize = myFiles[fileIndex] > > # normalize this to create eset > > normalized = SCAN(fileToNormalize) > > # create unique output name to save > > outFileName <- paste(fileToNormalize,".Rdata",sep="") > > save(normalized,file=outFileName) > > My problem is now an R one, but related to this problem. "normalized" must > be given a unique name so that when I load > all the esets back in they have different names. > > Any suggestions? > > > > > On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche@gmail.com> >wrote: > > > qux <- combine(foo, bar, baz) > > > > if foo, bar, and baz are all ExpressionSets (or other eSets of suitable > > mien) with the same fData rows and pData columns. > > > > I did this the other day for a huge GEO dataset that came as 3 separate > > Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of > > course) > > > > > > > > On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah@gmail.com> >wrote: > > > >> Thanks Ryan. I'll try this out. What if the esets are already generated. > >> So > >> I have a bunch laying > >> around. I'll look into your answer more and see if I can apply it to > this > >> situation. > >> > >> > >> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct@thompsonclan.org> >> >wrote: > >> > >> > celfiles <- list.files(pattern=".*\\.CEL$"**) > >> > >> > scan.esets <- lapply(celfiles, SCAN) > >> > scan.eset <- Reduce(combine, scan.esets) > >> > > >> > I forget what package the "combine" function is from, but I assume > it's > >> > the same package that provides the ExpressionSet class. > >> > > >> > > >> > > >> > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: > >> > > >> >> All, > >> >> > >> >> SCAN outputs an ExpressionSet object for each CEL file. What is a > nicer > >> >> way > >> >> to put them all into a matrix other than converting each one to a > >> vector > >> >> and then cbinding after each conversion? > >> >> > >> >> Thanks, > >> >> > >> >> Juliet > >> >> > >> >> [[alternative HTML version deleted]] > >> >> > >> >> ______________________________**_________________ > >> >> Bioconductor mailing list > >> >> Bioconductor@r-project.org > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > >> https://stat.ethz.ch/mailman/listinfo/bioconductor> > >> >> Search the archives: http://news.gmane.org/gmane.** > >> >> science.biology.informatics.**conductor< > >> http://news.gmane.org/gmane.science.biology.informatics.conductor> > >> > >> >> > >> > > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > > -- > > *He that would live in peace and at ease, * > > *Must not speak all he knows, nor judge all he sees.* > > * > > * > > Benjamin Franklin, Poor Richard's Almanack< > http://archive.org/details/poorrichardsalma00franrich> > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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> Tim: I thought combine() has binary. I was curious about this, so I went and looked. It's binary in methods-eSet.R, or so it appears, but: library(GEOquery) gset <- getGEO('GSE40279') length(gset) ## [1] 3 sapply(gset, ncol) ## GSE40279_series_matrix-1.txt.gz.Samples ## 255 ## GSE40279_series_matrix-2.txt.gz.Samples ## 255 ## GSE40279_series_matrix-3.txt.gz.Samples ## 146 gset <- do.call(combine, gset) ## Error in as.vector(x, "character") : ## cannot coerce type 'closure' to vector of type 'character' gset <- combine(gset[[1]], gset[[2]], gset[[3]]) ## no problem ncol(gset) ## Samples ## 656 The part that baffles me is that I don't see anywhere that combine() would recurse in the source! On Sat, Aug 10, 2013 at 5:43 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Tim: I thought combine() has binary. > > Juliet: this often comes up. You can do > assign("NAME", object) > which is essentially equivalent to > NAME <- object > Then you can also get the object by > get("NAME") > > Kasper > > > > On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah <juliet.hannah@gmail.com>wrote: > >> Thanks Tim. >> >> I'm trying this out and looks like I did not think this through. So let's >> say I have several CEL files. >> >> I am spreading this out over a cluster. So I have >> >> myFiles = ("cel1.CEL","cel2,CEL") >> >> # pick one file >> >> fileToNormalize = myFiles[fileIndex] >> >> # normalize this to create eset >> >> normalized = SCAN(fileToNormalize) >> >> # create unique output name to save >> >> outFileName <- paste(fileToNormalize,".Rdata",sep="") >> >> save(normalized,file=outFileName) >> >> My problem is now an R one, but related to this problem. "normalized" must >> be given a unique name so that when I load >> all the esets back in they have different names. >> >> Any suggestions? >> >> >> >> >> On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche@gmail.com>> >wrote: >> >> > qux <- combine(foo, bar, baz) >> > >> > if foo, bar, and baz are all ExpressionSets (or other eSets of suitable >> > mien) with the same fData rows and pData columns. >> > >> > I did this the other day for a huge GEO dataset that came as 3 separate >> > Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of >> > course) >> > >> > >> > >> > On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah@gmail.com>> >wrote: >> > >> >> Thanks Ryan. I'll try this out. What if the esets are already >> generated. >> >> So >> >> I have a bunch laying >> >> around. I'll look into your answer more and see if I can apply it to >> this >> >> situation. >> >> >> >> >> >> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct@thompsonclan.org>> >> >wrote: >> >> >> >> > celfiles <- list.files(pattern=".*\\.CEL$"**) >> >> >> >> > scan.esets <- lapply(celfiles, SCAN) >> >> > scan.eset <- Reduce(combine, scan.esets) >> >> > >> >> > I forget what package the "combine" function is from, but I assume >> it's >> >> > the same package that provides the ExpressionSet class. >> >> > >> >> > >> >> > >> >> > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: >> >> > >> >> >> All, >> >> >> >> >> >> SCAN outputs an ExpressionSet object for each CEL file. What is a >> nicer >> >> >> way >> >> >> to put them all into a matrix other than converting each one to a >> >> vector >> >> >> and then cbinding after each conversion? >> >> >> >> >> >> Thanks, >> >> >> >> >> >> Juliet >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> >> >> ______________________________**_________________ >> >> >> Bioconductor mailing list >> >> >> Bioconductor@r-project.org >> >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor> >> >> >> Search the archives: http://news.gmane.org/gmane.** >> >> >> science.biology.informatics.**conductor< >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >> >> >> >> >> >> > >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor@r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > >> > >> > >> > -- >> > *He that would live in peace and at ease, * >> > *Must not speak all he knows, nor judge all he sees.* >> > * >> > * >> > Benjamin Franklin, Poor Richard's Almanack< >> http://archive.org/details/poorrichardsalma00franrich> >> >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* * * Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> [[alternative HTML version deleted]]
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On 08/13/2013 04:24 PM, Tim Triche, Jr. wrote: >> Tim: I thought combine() has binary. > > I was curious about this, so I went and looked. It's binary in > methods-eSet.R, or so it appears, but: > > library(GEOquery) > gset <- getGEO('GSE40279') > length(gset) > ## [1] 3 > sapply(gset, ncol) > ## GSE40279_series_matrix-1.txt.gz.Samples > ## 255 > ## GSE40279_series_matrix-2.txt.gz.Samples > ## 255 > ## GSE40279_series_matrix-3.txt.gz.Samples > ## 146 > gset <- do.call(combine, gset) > ## Error in as.vector(x, "character") : > ## cannot coerce type 'closure' to vector of type 'character' > gset <- combine(gset[[1]], gset[[2]], gset[[3]]) > ## no problem > ncol(gset) > ## Samples > ## 656 > > The part that baffles me is that I don't see anywhere that combine() would > recurse in the source! It's the generic that does the magic > getGeneric("combine") nonstandardGenericFunction for "combine" defined from package "BiocGenerics" function (x, y, ...) { if (length(list(...)) > 0L) { callGeneric(x, do.call(callGeneric, list(y, ...))) } else { standardGeneric("combine") } } <environment: 0x646ceb0=""> Methods may be defined for arguments: x, y Use showMethods("combine") for currently available ones. > > > > On Sat, Aug 10, 2013 at 5:43 PM, Kasper Daniel Hansen < > kasperdanielhansen at gmail.com> wrote: > >> Tim: I thought combine() has binary. >> >> Juliet: this often comes up. You can do >> assign("NAME", object) >> which is essentially equivalent to >> NAME <- object >> Then you can also get the object by >> get("NAME") >> >> Kasper >> >> >> >> On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah <juliet.hannah at="" gmail.com="">wrote: >> >>> Thanks Tim. >>> >>> I'm trying this out and looks like I did not think this through. So let's >>> say I have several CEL files. >>> >>> I am spreading this out over a cluster. So I have >>> >>> myFiles = ("cel1.CEL","cel2,CEL") >>> >>> # pick one file >>> >>> fileToNormalize = myFiles[fileIndex] >>> >>> # normalize this to create eset >>> >>> normalized = SCAN(fileToNormalize) >>> >>> # create unique output name to save >>> >>> outFileName <- paste(fileToNormalize,".Rdata",sep="") >>> >>> save(normalized,file=outFileName) >>> >>> My problem is now an R one, but related to this problem. "normalized" must >>> be given a unique name so that when I load >>> all the esets back in they have different names. >>> >>> Any suggestions? >>> >>> >>> >>> >>> On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche at="" gmail.com="">>>> wrote: >>> >>>> qux <- combine(foo, bar, baz) >>>> >>>> if foo, bar, and baz are all ExpressionSets (or other eSets of suitable >>>> mien) with the same fData rows and pData columns. >>>> >>>> I did this the other day for a huge GEO dataset that came as 3 separate >>>> Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of >>>> course) >>>> >>>> >>>> >>>> On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah at="" gmail.com="">>>> wrote: >>>> >>>>> Thanks Ryan. I'll try this out. What if the esets are already >>> generated. >>>>> So >>>>> I have a bunch laying >>>>> around. I'll look into your answer more and see if I can apply it to >>> this >>>>> situation. >>>>> >>>>> >>>>> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct at="" thompsonclan.org="">>>>>> wrote: >>>>> >>>>>> celfiles <- list.files(pattern=".*\\.CEL$"**) >>>>> >>>>>> scan.esets <- lapply(celfiles, SCAN) >>>>>> scan.eset <- Reduce(combine, scan.esets) >>>>>> >>>>>> I forget what package the "combine" function is from, but I assume >>> it's >>>>>> the same package that provides the ExpressionSet class. >>>>>> >>>>>> >>>>>> >>>>>> On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: >>>>>> >>>>>>> All, >>>>>>> >>>>>>> SCAN outputs an ExpressionSet object for each CEL file. What is a >>> nicer >>>>>>> way >>>>>>> to put them all into a matrix other than converting each one to a >>>>> vector >>>>>>> and then cbinding after each conversion? >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Juliet >>>>>>> >>>>>>> [[alternative HTML version deleted]] >>>>>>> >>>>>>> ______________________________**_________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor> >>>>>>> Search the archives: http://news.gmane.org/gmane.** >>>>>>> science.biology.informatics.**conductor< >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor> >>>>> >>>>>>> >>>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>>> >>>> >>>> -- >>>> *He that would live in peace and at ease, * >>>> *Must not speak all he knows, nor judge all he sees.* >>>> * >>>> * >>>> Benjamin Franklin, Poor Richard's Almanack< >>> http://archive.org/details/poorrichardsalma00franrich> >>> >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> > > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Now I remember where I'd seen it before. Thanks! On Tue, Aug 13, 2013 at 4:26 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 08/13/2013 04:24 PM, Tim Triche, Jr. wrote: > >> Tim: I thought combine() has binary. >>> >> >> I was curious about this, so I went and looked. It's binary in >> methods-eSet.R, or so it appears, but: >> >> library(GEOquery) >> gset <- getGEO('GSE40279') >> length(gset) >> ## [1] 3 >> sapply(gset, ncol) >> ## GSE40279_series_matrix-1.txt.**gz.Samples >> ## 255 >> ## GSE40279_series_matrix-2.txt.**gz.Samples >> ## 255 >> ## GSE40279_series_matrix-3.txt.**gz.Samples >> ## 146 >> gset <- do.call(combine, gset) >> ## Error in as.vector(x, "character") : >> ## cannot coerce type 'closure' to vector of type 'character' >> gset <- combine(gset[[1]], gset[[2]], gset[[3]]) >> ## no problem >> ncol(gset) >> ## Samples >> ## 656 >> >> The part that baffles me is that I don't see anywhere that combine() would >> recurse in the source! >> > > It's the generic that does the magic > > > getGeneric("combine") > nonstandardGenericFunction for "combine" defined from package > "BiocGenerics" > > function (x, y, ...) > { > if (length(list(...)) > 0L) { > callGeneric(x, do.call(callGeneric, list(y, ...))) > } > else { > standardGeneric("combine") > } > } > <environment: 0x646ceb0=""> > Methods may be defined for arguments: x, y > Use showMethods("combine") for currently available ones. > > > >> >> >> On Sat, Aug 10, 2013 at 5:43 PM, Kasper Daniel Hansen < >> kasperdanielhansen@gmail.com> wrote: >> >> Tim: I thought combine() has binary. >>> >>> Juliet: this often comes up. You can do >>> assign("NAME", object) >>> which is essentially equivalent to >>> NAME <- object >>> Then you can also get the object by >>> get("NAME") >>> >>> Kasper >>> >>> >>> >>> On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah <juliet.hannah@gmail.com>* >>> *wrote: >>> >>> Thanks Tim. >>>> >>>> I'm trying this out and looks like I did not think this through. So >>>> let's >>>> say I have several CEL files. >>>> >>>> I am spreading this out over a cluster. So I have >>>> >>>> myFiles = ("cel1.CEL","cel2,CEL") >>>> >>>> # pick one file >>>> >>>> fileToNormalize = myFiles[fileIndex] >>>> >>>> # normalize this to create eset >>>> >>>> normalized = SCAN(fileToNormalize) >>>> >>>> # create unique output name to save >>>> >>>> outFileName <- paste(fileToNormalize,".Rdata"**,sep="") >>>> >>>> save(normalized,file=**outFileName) >>>> >>>> My problem is now an R one, but related to this problem. "normalized" >>>> must >>>> be given a unique name so that when I load >>>> all the esets back in they have different names. >>>> >>>> Any suggestions? >>>> >>>> >>>> >>>> >>>> On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche@gmail.com>>>> >>>>> wrote: >>>>> >>>> >>>> qux <- combine(foo, bar, baz) >>>>> >>>>> if foo, bar, and baz are all ExpressionSets (or other eSets of suitable >>>>> mien) with the same fData rows and pData columns. >>>>> >>>>> I did this the other day for a huge GEO dataset that came as 3 separate >>>>> Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of >>>>> course) >>>>> >>>>> >>>>> >>>>> On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah < >>>>> juliet.hannah@gmail.com >>>>> wrote: >>>>> >>>>> Thanks Ryan. I'll try this out. What if the esets are already >>>>>> >>>>> generated. >>>> >>>>> So >>>>>> I have a bunch laying >>>>>> around. I'll look into your answer more and see if I can apply it to >>>>>> >>>>> this >>>> >>>>> situation. >>>>>> >>>>>> >>>>>> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson < >>>>>> rct@thompsonclan.org >>>>>> >>>>>>> wrote: >>>>>>> >>>>>> >>>>>> celfiles <- list.files(pattern=".*\\.CEL$"****) >>>>>>> >>>>>> >>>>>> scan.esets <- lapply(celfiles, SCAN) >>>>>>> scan.eset <- Reduce(combine, scan.esets) >>>>>>> >>>>>>> I forget what package the "combine" function is from, but I assume >>>>>>> >>>>>> it's >>>> >>>>> the same package that provides the ExpressionSet class. >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: >>>>>>> >>>>>>> All, >>>>>>>> >>>>>>>> SCAN outputs an ExpressionSet object for each CEL file. What is a >>>>>>>> >>>>>>> nicer >>>> >>>>> way >>>>>>>> to put them all into a matrix other than converting each one to a >>>>>>>> >>>>>>> vector >>>>>> >>>>>>> and then cbinding after each conversion? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Juliet >>>>>>>> >>>>>>>> [[alternative HTML version deleted]] >>>>>>>> >>>>>>>> ______________________________****_________________ >>>>>>>> Bioconductor mailing list >>>>>>>> Bioconductor@r-project.org >>>>>>>> https://stat.ethz.ch/mailman/****listinfo/bioconductor<https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor=""> >>>>>>>> < >>>>>>>> >>>>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: s="" tat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>>> > >>>>>> >>>>>>> Search the archives: http://news.gmane.org/gmane.** >>>>>>>> science.biology.informatics.****conductor< >>>>>>>> >>>>>>> http://news.gmane.org/gmane.**science.biology.informatics.** >>>>>> conductor<http: news.gmane.org="" gmane.science.biology.informati="" cs.conductor=""> >>>>>> > >>>>>> >>>>>> >>>>>>>> >>>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> ______________________________**_________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org >>>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: st="" at.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.**science.biology.informatics.**con ductor<http: news.gmane.org="" gmane.science.biology.informatics.conduct="" or=""> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> *He that would live in peace and at ease, * >>>>> *Must not speak all he knows, nor judge all he sees.* >>>>> * >>>>> * >>>>> Benjamin Franklin, Poor Richard's Almanack< >>>>> >>>> http://archive.org/details/**poorrichardsalma00franrich<http: ar="" chive.org="" details="" poorrichardsalma00franrich=""> >>>> > >>>> >>>> >>>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.**science.biology.informatics.**condu ctor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>> >>>> >>> >>> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > -- *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* * * Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> [[alternative HTML version deleted]]
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Btw, I have started to use combineList as an alias for a method that works on a list in a faster way. Depending on context, this may be much faster than Reduce(). For example with SummarizedExperiments where the rowData are all equal. Martin: it seems like we have started to go away from combine() as the general combine two datasets and instead are using cbind/rbind for SummarizedExperiment, or am I missing something? (Probably am). Kasper On Tue, Aug 13, 2013 at 7:33 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > Now I remember where I'd seen it before. Thanks! > > > > On Tue, Aug 13, 2013 at 4:26 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > >> On 08/13/2013 04:24 PM, Tim Triche, Jr. wrote: >> >>> Tim: I thought combine() has binary. >>>> >>> >>> I was curious about this, so I went and looked. It's binary in >>> methods-eSet.R, or so it appears, but: >>> >>> library(GEOquery) >>> gset <- getGEO('GSE40279') >>> length(gset) >>> ## [1] 3 >>> sapply(gset, ncol) >>> ## GSE40279_series_matrix-1.txt.**gz.Samples >>> ## 255 >>> ## GSE40279_series_matrix-2.txt.**gz.Samples >>> ## 255 >>> ## GSE40279_series_matrix-3.txt.**gz.Samples >>> ## 146 >>> gset <- do.call(combine, gset) >>> ## Error in as.vector(x, "character") : >>> ## cannot coerce type 'closure' to vector of type 'character' >>> gset <- combine(gset[[1]], gset[[2]], gset[[3]]) >>> ## no problem >>> ncol(gset) >>> ## Samples >>> ## 656 >>> >>> The part that baffles me is that I don't see anywhere that combine() >>> would >>> recurse in the source! >>> >> >> It's the generic that does the magic >> >> > getGeneric("combine") >> nonstandardGenericFunction for "combine" defined from package >> "BiocGenerics" >> >> function (x, y, ...) >> { >> if (length(list(...)) > 0L) { >> callGeneric(x, do.call(callGeneric, list(y, ...))) >> } >> else { >> standardGeneric("combine") >> } >> } >> <environment: 0x646ceb0=""> >> Methods may be defined for arguments: x, y >> Use showMethods("combine") for currently available ones. >> >> >> >>> >>> >>> On Sat, Aug 10, 2013 at 5:43 PM, Kasper Daniel Hansen < >>> kasperdanielhansen@gmail.com> wrote: >>> >>> Tim: I thought combine() has binary. >>>> >>>> Juliet: this often comes up. You can do >>>> assign("NAME", object) >>>> which is essentially equivalent to >>>> NAME <- object >>>> Then you can also get the object by >>>> get("NAME") >>>> >>>> Kasper >>>> >>>> >>>> >>>> On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah <juliet.hannah@gmail.com> >>>> **wrote: >>>> >>>> Thanks Tim. >>>>> >>>>> I'm trying this out and looks like I did not think this through. So >>>>> let's >>>>> say I have several CEL files. >>>>> >>>>> I am spreading this out over a cluster. So I have >>>>> >>>>> myFiles = ("cel1.CEL","cel2,CEL") >>>>> >>>>> # pick one file >>>>> >>>>> fileToNormalize = myFiles[fileIndex] >>>>> >>>>> # normalize this to create eset >>>>> >>>>> normalized = SCAN(fileToNormalize) >>>>> >>>>> # create unique output name to save >>>>> >>>>> outFileName <- paste(fileToNormalize,".Rdata"**,sep="") >>>>> >>>>> save(normalized,file=**outFileName) >>>>> >>>>> My problem is now an R one, but related to this problem. "normalized" >>>>> must >>>>> be given a unique name so that when I load >>>>> all the esets back in they have different names. >>>>> >>>>> Any suggestions? >>>>> >>>>> >>>>> >>>>> >>>>> On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche@gmail.com>>>>> >>>>>> wrote: >>>>>> >>>>> >>>>> qux <- combine(foo, bar, baz) >>>>>> >>>>>> if foo, bar, and baz are all ExpressionSets (or other eSets of >>>>>> suitable >>>>>> mien) with the same fData rows and pData columns. >>>>>> >>>>>> I did this the other day for a huge GEO dataset that came as 3 >>>>>> separate >>>>>> Esets off of getGEO. (Then I turned it into a SummarizedExperiment, >>>>>> of >>>>>> course) >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah < >>>>>> juliet.hannah@gmail.com >>>>>> wrote: >>>>>> >>>>>> Thanks Ryan. I'll try this out. What if the esets are already >>>>>>> >>>>>> generated. >>>>> >>>>>> So >>>>>>> I have a bunch laying >>>>>>> around. I'll look into your answer more and see if I can apply it to >>>>>>> >>>>>> this >>>>> >>>>>> situation. >>>>>>> >>>>>>> >>>>>>> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson < >>>>>>> rct@thompsonclan.org >>>>>>> >>>>>>>> wrote: >>>>>>>> >>>>>>> >>>>>>> celfiles <- list.files(pattern=".*\\.CEL$"****) >>>>>>>> >>>>>>> >>>>>>> scan.esets <- lapply(celfiles, SCAN) >>>>>>>> scan.eset <- Reduce(combine, scan.esets) >>>>>>>> >>>>>>>> I forget what package the "combine" function is from, but I assume >>>>>>>> >>>>>>> it's >>>>> >>>>>> the same package that provides the ExpressionSet class. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: >>>>>>>> >>>>>>>> All, >>>>>>>>> >>>>>>>>> SCAN outputs an ExpressionSet object for each CEL file. What is a >>>>>>>>> >>>>>>>> nicer >>>>> >>>>>> way >>>>>>>>> to put them all into a matrix other than converting each one to a >>>>>>>>> >>>>>>>> vector >>>>>>> >>>>>>>> and then cbinding after each conversion? >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Juliet >>>>>>>>> >>>>>>>>> [[alternative HTML version deleted]] >>>>>>>>> >>>>>>>>> ______________________________****_________________ >>>>>>>>> Bioconductor mailing list >>>>>>>>> Bioconductor@r-project.org >>>>>>>>> https://stat.ethz.ch/mailman/****listinfo/bioconductor<https :="" stat.ethz.ch="" mailman="" **listinfo="" bioconductor=""> >>>>>>>>> < >>>>>>>>> >>>>>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>>>> > >>>>>>> >>>>>>>> Search the archives: http://news.gmane.org/gmane.** >>>>>>>>> science.biology.informatics.****conductor< >>>>>>>>> >>>>>>>> http://news.gmane.org/gmane.**science.biology.informatics.** >>>>>>> conductor<http: news.gmane.org="" gmane.science.biology.informat="" ics.conductor=""> >>>>>>> > >>>>>>> >>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> [[alternative HTML version deleted]] >>>>>>> >>>>>>> ______________________________**_________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor@r-project.org >>>>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: s="" tat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.**science.biology.informatics.** >>>>>>> conductor<http: news.gmane.org="" gmane.science.biology.informat="" ics.conductor=""> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> *He that would live in peace and at ease, * >>>>>> *Must not speak all he knows, nor judge all he sees.* >>>>>> * >>>>>> * >>>>>> Benjamin Franklin, Poor Richard's Almanack< >>>>>> >>>>> http://archive.org/details/**poorrichardsalma00franrich<http: a="" rchive.org="" details="" poorrichardsalma00franrich=""> >>>>> > >>>>> >>>>> >>>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> ______________________________**_________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.**science.biology.informatics.**cond uctor<http: news.gmane.org="" gmane.science.biology.informatics.conducto="" r=""> >>>>> >>>>> >>>> >>>> >>> >>> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> > > > > -- > *He that would live in peace and at ease, * > *Must not speak all he knows, nor judge all he sees.* > * > * > Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> > [[alternative HTML version deleted]]
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On 08/13/2013 09:47 PM, Kasper Daniel Hansen wrote: > Btw, I have started to use combineList as an alias for a method that works on a > list in a faster way. Depending on context, this may be much faster than > Reduce(). For example with SummarizedExperiments where the rowData are all equal. > > Martin: it seems like we have started to go away from combine() as the general > combine two datasets and instead are using cbind/rbind for SummarizedExperiment, > or am I missing something? (Probably am). combine's semantics are more complicated than cbind or rbind > m <- matrix(1:20, nrow=5, dimnames=list(LETTERS[1:5], letters[1:4])) > combine(m[1:3, 1:3], m[3:5, 3:4]) # overlap a b c d A 1 6 11 NA B 2 7 12 NA C 3 8 13 18 D NA NA 14 19 E NA NA 15 20 In the end I'm always amazed that the implementations do close enough to the right thing that people either don't complain or don't notice that it's not exactly what they want. Personally I think it's better to leave all this cleverness in the hands of the user. Martin > > Kasper > > > On Tue, Aug 13, 2013 at 7:33 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> <mailto:tim.triche at="" gmail.com="">> wrote: > > Now I remember where I'd seen it before. Thanks! > > > > On Tue, Aug 13, 2013 at 4:26 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 08/13/2013 04:24 PM, Tim Triche, Jr. wrote: > > Tim: I thought combine() has binary. > > > I was curious about this, so I went and looked. It's binary in > methods-eSet.R, or so it appears, but: > > library(GEOquery) > gset <- getGEO('GSE40279') > length(gset) > ## [1] 3 > sapply(gset, ncol) > ## GSE40279_series_matrix-1.txt.__gz.Samples > ## 255 > ## GSE40279_series_matrix-2.txt.__gz.Samples > ## 255 > ## GSE40279_series_matrix-3.txt.__gz.Samples > ## 146 > gset <- do.call(combine, gset) > ## Error in as.vector(x, "character") : > ## cannot coerce type 'closure' to vector of type 'character' > gset <- combine(gset[[1]], gset[[2]], gset[[3]]) > ## no problem > ncol(gset) > ## Samples > ## 656 > > The part that baffles me is that I don't see anywhere that combine() > would > recurse in the source! > > > It's the generic that does the magic > > > getGeneric("combine") > nonstandardGenericFunction for "combine" defined from package "BiocGenerics" > > function (x, y, ...) > { > if (length(list(...)) > 0L) { > callGeneric(x, do.call(callGeneric, list(y, ...))) > } > else { > standardGeneric("combine") > } > } > <environment: 0x646ceb0=""> > Methods may be defined for arguments: x, y > Use showMethods("combine") for currently available ones. > > > > > > On Sat, Aug 10, 2013 at 5:43 PM, Kasper Daniel Hansen < > kasperdanielhansen at gmail.com <mailto:kasperdanielhansen at="" gmail.com="">> > wrote: > > Tim: I thought combine() has binary. > > Juliet: this often comes up. You can do > assign("NAME", object) > which is essentially equivalent to > NAME <- object > Then you can also get the object by > get("NAME") > > Kasper > > > > On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah > <juliet.hannah at="" gmail.com="" <mailto:juliet.hannah="" at="" gmail.com="">>__wrote: > > Thanks Tim. > > I'm trying this out and looks like I did not think this > through. So let's > say I have several CEL files. > > I am spreading this out over a cluster. So I have > > myFiles = ("cel1.CEL","cel2,CEL") > > # pick one file > > fileToNormalize = myFiles[fileIndex] > > # normalize this to create eset > > normalized = SCAN(fileToNormalize) > > # create unique output name to save > > outFileName <- paste(fileToNormalize,".Rdata"__,sep="") > > save(normalized,file=__outFileName) > > My problem is now an R one, but related to this problem. > "normalized" must > be given a unique name so that when I load > all the esets back in they have different names. > > Any suggestions? > > > > > On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. > <tim.triche at="" gmail.com="" <mailto:tim.triche="" at="" gmail.com=""> > > wrote: > > > qux <- combine(foo, bar, baz) > > if foo, bar, and baz are all ExpressionSets (or other > eSets of suitable > mien) with the same fData rows and pData columns. > > I did this the other day for a huge GEO dataset that > came as 3 separate > Esets off of getGEO. (Then I turned it into a > SummarizedExperiment, of > course) > > > > On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah > <juliet.hannah at="" gmail.com="" <mailto:juliet.hannah="" at="" gmail.com=""> > wrote: > > Thanks Ryan. I'll try this out. What if the esets > are already > > generated. > > So > I have a bunch laying > around. I'll look into your answer more and see if I > can apply it to > > this > > situation. > > > On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson > <rct at="" thompsonclan.org="" <mailto:rct="" at="" thompsonclan.org=""> > > wrote: > > > celfiles <- list.files(pattern=".*\\.CEL$"__**) > > > scan.esets <- lapply(celfiles, SCAN) > scan.eset <- Reduce(combine, scan.esets) > > I forget what package the "combine" function is > from, but I assume > > it's > > the same package that provides the ExpressionSet > class. > > > > On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet > Hannah wrote: > > All, > > SCAN outputs an ExpressionSet object for > each CEL file. What is a > > nicer > > way > to put them all into a matrix other than > converting each one to a > > vector > > and then cbinding after each conversion? > > Thanks, > > Juliet > > [[alternative HTML version deleted]] > > ________________________________**_________________ > Bioconductor mailing list > Bioconductor at r-project.org > <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/*__*listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor="">< > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">> > > Search the archives: > http://news.gmane.org/gmane.** > science.biology.informatics.**__conductor< > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor="">> > > > > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > -- > *He that would live in peace and at ease, * > *Must not speak all he knows, nor judge all he sees.* > * > * > Benjamin Franklin, Poor Richard's Almanack< > > http://archive.org/details/__poorrichardsalma00franrich > <http: archive.org="" details="" poorrichardsalma00franrich="">> > > > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 <tel:%28206%29%20667-2793> > > > > > -- > /He that would live in peace and at ease, / > /Must not speak all he knows, nor judge all he sees./ > / > / > Benjamin Franklin, Poor Richard's Almanack > <http: archive.org="" details="" poorrichardsalma00franrich=""> > > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Steve, Will you take a look at this thread and make any other suggestions. Thanks! Evan On Aug 10, 2013, at 6:00 AM, <bioconductor-request at="" r-project.org=""> wrote: > Date: Fri, 9 Aug 2013 13:00:38 -0700 > From: "Tim Triche, Jr." <tim.triche at="" gmail.com=""> > To: Juliet Hannah <juliet.hannah at="" gmail.com=""> > Cc: Bioconductor mailing list <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] combining/merging several ExpressionSet objects > from SCAN > Message-ID: > <cac+n9bxazjisyeauduyzwb37xtt5lertj3mpe1fcatetnw0x2w at="" mail.gmail.com=""> > Content-Type: text/plain > > use saveRDS(foo, file='foo.rds') and then when you reload it with readRDS, > the resulting object can have whatever name you like. > > > > > On Fri, Aug 9, 2013 at 12:47 PM, Juliet Hannah <juliet.hannah at="" gmail.com="">wrote: > >> Thanks Tim. >> >> I'm trying this out and looks like I did not think this through. So let's >> say I have several CEL files. >> >> I am spreading this out over a cluster. So I have >> >> myFiles = ("cel1.CEL","cel2,CEL") >> >> # pick one file >> >> fileToNormalize = myFiles[fileIndex] >> >> # normalize this to create eset >> >> normalized = SCAN(fileToNormalize) >> >> # create unique output name to save >> >> outFileName <- paste(fileToNormalize,".Rdata",sep="") >> >> save(normalized,file=outFileName) >> >> My problem is now an R one, but related to this problem. "normalized" must >> be given a unique name so that when I load >> all the esets back in they have different names. >> >> Any suggestions? >> >> >> >> >> On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche at="" gmail.com="">wrote: >> >>> qux <- combine(foo, bar, baz) >>> >>> if foo, bar, and baz are all ExpressionSets (or other eSets of suitable >>> mien) with the same fData rows and pData columns. >>> >>> I did this the other day for a huge GEO dataset that came as 3 separate >>> Esets off of getGEO. (Then I turned it into a SummarizedExperiment, of >>> course) >>> >>> >>> >>> On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah at="" gmail.com="">wrote: >>> >>>> Thanks Ryan. I'll try this out. What if the esets are already generated. >>>> So >>>> I have a bunch laying >>>> around. I'll look into your answer more and see if I can apply it to this >>>> situation. >>>> >>>> >>>> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct at="" thompsonclan.org="">>>>> wrote: >>>> >>>>> celfiles <- list.files(pattern=".*\\.CEL$"**) >>>> >>>>> scan.esets <- lapply(celfiles, SCAN) >>>>> scan.eset <- Reduce(combine, scan.esets) >>>>> >>>>> I forget what package the "combine" function is from, but I assume it's >>>>> the same package that provides the ExpressionSet class. >>>>> >>>>> >>>>> >>>>> On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote: >>>>> >>>>>> All, >>>>>> >>>>>> SCAN outputs an ExpressionSet object for each CEL file. What is a >>>> nicer >>>>>> way >>>>>> to put them all into a matrix other than converting each one to a >>>> vector >>>>>> and then cbinding after each conversion? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Juliet >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> ______________________________**_________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor> >>>>>> Search the archives: http://news.gmane.org/gmane.** >>>>>> science.biology.informatics.**conductor< >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor> >>>> >>>>>> >>>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >>> >>> -- >>> *He that would live in peace and at ease, * >>> *Must not speak all he knows, nor judge all he sees.* >>> * >>> * >>> Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> >>> >> >> > > > -- > *He that would live in peace and at ease, * > *Must not speak all he knows, nor judge all he sees.* > * > * > Benjamin Franklin, Poor Richard's > Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> > > [[alternative HTML version deleted]]
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