Affycoretools - Limit genes in Venn diagram by fold change?

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Quentin Anstee ▴ 110

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ADD COMMENT • link updated 18.9 years ago by James W. MacDonald 67k • written 18.9 years ago by Quentin Anstee ▴ 110

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James W. MacDonald 67k

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Hi Quentin, Quentin Anstee wrote: > Dear List, > > Having processed my affy data and fitted a linear model with limma, I would > like to export a Venn diagram to illustrate the number of genes in each of > my 3 comparisons. I have used the following script which outputs all the > genes that are significantly differentially expressed and is based on the > affycoretools package: > > rslt<-decideTests(fit2, adjust.method="fdr") > vc<-vennCounts2(rslt,method="both") > vennDiagram(vc,cex=0.8) > vennSelect(mySubSet,fit2,design,rslt,method="both") > > What I would like to do is to reduce the number of genes that are counted in > the Venn diagram so that only those with a 1.5 fold increase or decrease in > expression are included. > > Please could you advise me how this can be achieved? I would think something like: idx <- abs(fit2$coefficients) > 1.5 rslt <- rslt * idx vennSelect(mySubSet, fit2, design, rslt, method = "both") would do it. HTH, Jim > > Very many thanks, > > Quentin > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

ADD COMMENT • link 18.9 years ago James W. MacDonald 67k

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James W. MacDonald wrote: > Hi Quentin, > > Quentin Anstee wrote: > >>Dear List, >> >>Having processed my affy data and fitted a linear model with limma, I would >>like to export a Venn diagram to illustrate the number of genes in each of >>my 3 comparisons. I have used the following script which outputs all the >>genes that are significantly differentially expressed and is based on the >>affycoretools package: >> >>rslt<-decideTests(fit2, adjust.method="fdr") >>vc<-vennCounts2(rslt,method="both") >>vennDiagram(vc,cex=0.8) >>vennSelect(mySubSet,fit2,design,rslt,method="both") >> >>What I would like to do is to reduce the number of genes that are counted in >>the Venn diagram so that only those with a 1.5 fold increase or decrease in >>expression are included. >> >>Please could you advise me how this can be achieved? > > > I would think something like: > > idx <- abs(fit2$coefficients) > 1.5 Hmmm. Make that idx <- abs(fit2$coefficients) > log2(1.5) unless you really want a log difference of 1.5 rather than a 1.5 fold change. Jim > rslt <- rslt * idx > vennSelect(mySubSet, fit2, design, rslt, method = "both") > > would do it. > > HTH, > > Jim > > > >> >>Very many thanks, >> >>Quentin >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

ADD REPLY • link 18.9 years ago James W. MacDonald 67k

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Hi Jim, Thanks again! Quentin > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 03 March 2006 17:56 > Cc: Quentin Anstee; 'Bioconductor' > Subject: Re: [BioC] Affycoretools - Limit genes in Venn > diagram by fold change? > > James W. MacDonald wrote: > > Hi Quentin, > > > > Quentin Anstee wrote: > > > >>Dear List, > >> > >>Having processed my affy data and fitted a linear model > with limma, I > >>would like to export a Venn diagram to illustrate the > number of genes > >>in each of my 3 comparisons. I have used the following script which > >>outputs all the genes that are significantly differentially > expressed > >>and is based on the affycoretools package: > >> > >>rslt<-decideTests(fit2, adjust.method="fdr") > >>vc<-vennCounts2(rslt,method="both") > >>vennDiagram(vc,cex=0.8) > >>vennSelect(mySubSet,fit2,design,rslt,method="both") > >> > >>What I would like to do is to reduce the number of genes that are > >>counted in the Venn diagram so that only those with a 1.5 fold > >>increase or decrease in expression are included. > >> > >>Please could you advise me how this can be achieved? > > > > > > I would think something like: > > > > idx <- abs(fit2$coefficients) > 1.5 > > Hmmm. Make that > > idx <- abs(fit2$coefficients) > log2(1.5) > > unless you really want a log difference of 1.5 rather than a > 1.5 fold change. > > Jim > > > > > > rslt <- rslt * idx > > vennSelect(mySubSet, fit2, design, rslt, method = "both") > > > > would do it. > > > > HTH, > > > > Jim > > > > > > > >> > >>Very many thanks, > >> > >>Quentin > >> > >> [[alternative HTML version deleted]] > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor at stat.math.ethz.ch > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >

ADD REPLY • link 18.9 years ago Quentin Anstee ▴ 110

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