Hi Srinivas, On 1/24/2012 4:31 AM, Srinivas M. Srikanth wrote: > Hi all, > > I am working with two color microrray data and have three different stages > of cancer along with normal, all normalized with a universal Normal. I > analyzed the data using Limma package in R.My workflow is as below: > > library(limma) > targets<-readTargets(filename) > RG<-read.maimages(targets, > source="genepix") > RG$genes<-readGAL() > MA<-normalizeWithinArrays(RG,method="loess") > plotMA(RG) > plotMA(MA) > MA<-normalizeBetweenArrays(MA,method="aquantile") > design=modelMatrix(MA,ref="Control") > fit<-lmfit(MA,design) > fit2<-ebayes(fit) > contrastmatrix<-makeContrasts("StageI-Normal","StageII-Normal ","StageIII-Normal","StageIII-StageI","StageII-StageI","StageIII- StageII",levels=design) > fit3<-contrasts.fit(fit2,contrastsmatrix) > fit3<-ebayes(fi3) > results<- decideTests(fit3,method="global") > vennDiagram(results[,1:3]) > > I want to print the common genes which are common in all three stages and > also find common signature set of genes among different stages, please help > on how I should proceed further. There is a function vennSelect() in my affycoretools package that is designed to print out all the genes in each section of a Venn diagram. It is intended to annotate as well, so if you don't have an annotation package for your chip you will either need to make one, or you could debug() vennSelect() and grab the results before it gets to the point where it tries to annotate. I am not sure exactly what you mean by 'common signature set of genes'. Perhaps you should look at e.g., GSEABase, GOstats, Category, etc. All these packages have vignettes that you could read. Best, Jim > > > The target file is as below: > SampleNumber FileName Cy3 Cy5 > 1 CN 310_N.gpr Control Normal > 2 CN 314_N.gpr Control Normal > 3 CN 318_N.gpr Control Normal > 4 CN 321_N.gpr Control Normal > 5 CN 322_N.gpr Control Normal > 6 CT 1015_II.gpr Control StageII > 7 CT1021_II.gpr Control StageII > 8 CT 1063_II.gpr Control StageII > 9 CT1077_II.gpr Control StageII > 10 CT1099_III.gpr Control StageIII > 11 CT 1131_III.gpr Control StageIII > 12 CT 1138_I.gpr Control StageI > 13 CT 1178_III.gpr Control StageIII > 14 CT 1179_III.gpr Control StageIII > 15 CT 1187_III.gpr Control StageIII > 16 CT500_I.gpr Control StageI > 17 CT503_II.gpr Control StageII > 18 CT 510_I.gpr Control StageI > 19 CT 513_I.gpr Control StageI > 20 CT 514_I.gpr Control StageI > 21 CT 515_I.gpr Control StageI > 22 CT 800_II.gpr Control StageII > 23 CT 805_II.gpr Control StageII > 24 CT 809_III.gpr Control StageIII > 25 CT 833_I.gpr Control StageI > 26 CT 843_I.gpr Control StageI > 27 CT 859_III.gpr Control StageIII > 28 CT 871_II.gpr Control StageII > 29 CT 905_III.gpr Control StageIII > 30 CT 935_II.gpr Control StageII > > > Regards, > Srikanth > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Hi Srinivas, On 1/24/2012 4:31 AM, Srinivas M. Srikanth wrote: > Hi all, > > I am working with two color microrray data and have three different stages > of cancer along with normal, all normalized with a universal Normal. I > analyzed the data using Limma package in R.My workflow is as below: > > library(limma) > targets<-readTargets(filename) > RG<-read.maimages(targets, > source="genepix") > RG$genes<-readGAL() > MA<-normalizeWithinArrays(RG,method="loess") > plotMA(RG) > plotMA(MA) > MA<-normalizeBetweenArrays(MA,method="aquantile") > design=modelMatrix(MA,ref="Control") > fit<-lmfit(MA,design) > fit2<-ebayes(fit) > contrastmatrix<-makeContrasts("StageI-Normal","StageII-Normal ","StageIII-Normal","StageIII-StageI","StageII-StageI","StageIII- StageII",levels=design) > fit3<-contrasts.fit(fit2,contrastsmatrix) > fit3<-ebayes(fi3) > results<- decideTests(fit3,method="global") > vennDiagram(results[,1:3]) > > I want to print the common genes which are common in all three stages and > also find common signature set of genes among different stages, please help > on how I should proceed further. There is a function vennSelect() in my affycoretools package that is designed to print out all the genes in each section of a Venn diagram. It is intended to annotate as well, so if you don't have an annotation package for your chip you will either need to make one, or you could debug() vennSelect() and grab the results before it gets to the point where it tries to annotate. I am not sure exactly what you mean by 'common signature set of genes'. Perhaps you should look at e.g., GSEABase, GOstats, Category, etc. All these packages have vignettes that you could read. Best, Jim > > > The target file is as below: > SampleNumber FileName Cy3 Cy5 > 1 CN 310_N.gpr Control Normal > 2 CN 314_N.gpr Control Normal > 3 CN 318_N.gpr Control Normal > 4 CN 321_N.gpr Control Normal > 5 CN 322_N.gpr Control Normal > 6 CT 1015_II.gpr Control StageII > 7 CT1021_II.gpr Control StageII > 8 CT 1063_II.gpr Control StageII > 9 CT1077_II.gpr Control StageII > 10 CT1099_III.gpr Control StageIII > 11 CT 1131_III.gpr Control StageIII > 12 CT 1138_I.gpr Control StageI > 13 CT 1178_III.gpr Control StageIII > 14 CT 1179_III.gpr Control StageIII > 15 CT 1187_III.gpr Control StageIII > 16 CT500_I.gpr Control StageI > 17 CT503_II.gpr Control StageII > 18 CT 510_I.gpr Control StageI > 19 CT 513_I.gpr Control StageI > 20 CT 514_I.gpr Control StageI > 21 CT 515_I.gpr Control StageI > 22 CT 800_II.gpr Control StageII > 23 CT 805_II.gpr Control StageII > 24 CT 809_III.gpr Control StageIII > 25 CT 833_I.gpr Control StageI > 26 CT 843_I.gpr Control StageI > 27 CT 859_III.gpr Control StageIII > 28 CT 871_II.gpr Control StageII > 29 CT 905_III.gpr Control StageIII > 30 CT 935_II.gpr Control StageII > > > Regards, > Srikanth > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues