That Venn Diagram is not very interesting in your case. The intercept will (unless you centered the data for some reason) always be significant and is of little interest. The comparison you are interested is between the groups. The empty circle in the diagram just means that you have no genes significant at an Benjamini-Hochberg adjusted p-value below 5%. That can happen if there are not many differential genes. You should look at the p-values for the group comparison, eg. look at the toptable for the second coefficient (that is the log-ratio between treatment and control)... If you want a picture, the p-value histogram gives you an overview (hist(fit.eBayes$p.value[,2],nclass=100) or something like that). If that has a peak at the left, it indicates that some genes are differentially expresse. If it is flat, it indicates that all your results might as well be chance. Probably it makes sense to work through one of the examples giving in the limma tutorial and make sure you know exactly what you are doing, before you go on with your own data... Claus > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Rohit Farmer > Sent: 16 March 2010 15:16 > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Reg: T-statistic using limma > > thanks Claus > > i did as u mentioned and got the results ... but when i am running > > results <- decideTests(fit) > and after that > > vennDiagram(results) > > the vendiagram shows two circles left one shows intercept > will the number of all the genes and the right one > population.goupsLLO contains zero value and the intersection > is also not showing contains zero how can i visualize my results.... > > > On Tue, Mar 16, 2010 at 7:29 PM, Rohit Farmer > <rohit.farmer at="" gmail.com=""> wrote: > > Hi there ... here i am trying to do a moderate t-statistics using > > limma i use the following code and got these results but my > process in > > not able to complete and showing some error at the end > > > >> population.goups > >> > <-factor(c('10LLO1.CEL','11LLO2.CEL','12LLO3.CEL','1Control1.CEL','2C > >> ontrol2.CEL','3Control3.CEL') > > + ) > >> population.goups > > [1] 10LLO1.CEL ? ?11LLO2.CEL ? ?12LLO3.CEL ? ?1Control1.CEL > > 2Control2.CEL 3Control3.CEL > > Levels: 10LLO1.CEL 11LLO2.CEL 12LLO3.CEL 1Control1.CEL > 2Control2.CEL > > 3Control3.CEL > >> design <- model.matrix (~population.groups) > > Error in eval(expr, envir, enclos) : object 'population.groups' not > > found > >> design <- model.matrix (~population.goups) design > > ?(Intercept) population.goups11LLO2.CEL population.goups12LLO3.CEL > > population.goups1Control1.CEL > > 1 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 > > ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 2 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 > > ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 3 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?1 > > ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 4 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 > > ? ? ? ? ? ? ? ? ? ? ? ? 1 > > 5 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 > > ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 6 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 > > ? ? ? ? ? ? ? ? ? ? ? ? 0 > > ?population.goups2Control2.CEL population.goups3Control3.CEL > > 1 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 2 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 3 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 4 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 5 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 > > 6 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 > > attr(,"assign") > > [1] 0 1 1 1 1 1 > > attr(,"contrasts") > > attr(,"contrasts")$population.goups > > [1] "contr.treatment" > > > >> fit <- lmFit(eset, design) > >> fit.ebayes <- eBayes(fit) > > Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = > > stdev.coef.lim) : > > ?No residual degrees of freedom in linear model fits > > > > > ---------------------------------------------------------------------- > > --- > > > > Please any help in this regard will be highly appreaciated > > > > > > Rohit > > > > > > > > -- > > Rohit Farmer > > M.Tech Bioinformatics > > Department of Computational Biology and Bioinformatics > Jacob School of > > Biengineering and Biotechnology Sam Higginbottom Institute of > > Agriculture, Technology and Sciences (Formerly known as Allahabad > > Agricultural Institute - Deemed University) Allahabad, UP, > INDIA - 211 > > 007 Ph. No. 9839845093, 9415261403 e-Mail > rohit.farmer at gmail.com Blog > > http://rohitsspace.blogspot.com > > > > > > -- > Rohit Farmer > M.Tech Bioinformatics > Department of Computational Biology and Bioinformatics Jacob > School of Biengineering and Biotechnology Sam Higginbottom > Institute of Agriculture, Technology and Sciences (Formerly > known as Allahabad Agricultural Institute - Deemed > University) Allahabad, UP, INDIA - 211 007 Ph. No. > 9839845093, 9415261403 e-Mail rohit.farmer at gmail.com Blog > http://rohitsspace.blogspot.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Thanks Claus once again u sorted out my problem actually i want to look for differential expression ... and i got it i believe ... actually right now i am graduate student only and dont know much theory behind microarray data analysis ...i am following a paper as a protocol and referring to manuals ... Next i want to go for clustering using different algorithms its the next objective of my semester project can u suggest me which library to use ... and a flow chart sort of ... you have been great help to me i was struggling since morning .. GOD bless Thanks Rohit On Tue, Mar 16, 2010 at 8:45 PM, Rohit Farmer <rohit.farmer at="" gmail.com=""> wrote: > thanks Claus > > i did as u mentioned and got the results ... but when i am running > > results <- decideTests(fit) > and after that > > vennDiagram(results) > > the vendiagram shows two circles left one shows intercept will the > number of all the genes and the right one population.goupsLLO contains > zero value and the intersection is also not showing contains zero how > can i visualize my results.... > > > On Tue, Mar 16, 2010 at 7:29 PM, Rohit Farmer <rohit.farmer at="" gmail.com=""> wrote: >> Hi there ... here i am trying to do a moderate t-statistics using >> limma i use the following code and got these results but my process in >> not able to complete and showing some error at the end >> >>> population.goups <-factor(c('10LLO1.CEL','11LLO2.CEL','12LLO3.CEL' ,'1Control1.CEL','2Control2.CEL','3Control3.CEL') >> + ) >>> population.goups >> [1] 10LLO1.CEL ? ?11LLO2.CEL ? ?12LLO3.CEL ? ?1Control1.CEL >> 2Control2.CEL 3Control3.CEL >> Levels: 10LLO1.CEL 11LLO2.CEL 12LLO3.CEL 1Control1.CEL 2Control2.CEL >> 3Control3.CEL >>> design <- model.matrix (~population.groups) >> Error in eval(expr, envir, enclos) : object 'population.groups' not found >>> design <- model.matrix (~population.goups) >>> design >> ?(Intercept) population.goups11LLO2.CEL population.goups12LLO3.CEL >> population.goups1Control1.CEL >> 1 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 >> ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 2 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 >> ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 3 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?1 >> ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 4 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 >> ? ? ? ? ? ? ? ? ? ? ? ? 1 >> 5 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 >> ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 6 ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ?0 ? ? ? ? ? ? ? ? ? ? ? ? ?0 >> ? ? ? ? ? ? ? ? ? ? ? ? 0 >> ?population.goups2Control2.CEL population.goups3Control3.CEL >> 1 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 2 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 3 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 4 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 5 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 >> 6 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 >> attr(,"assign") >> [1] 0 1 1 1 1 1 >> attr(,"contrasts") >> attr(,"contrasts")$population.goups >> [1] "contr.treatment" >> >>> fit <- lmFit(eset, design) >>> fit.ebayes <- eBayes(fit) >> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = >> stdev.coef.lim) : >> ?No residual degrees of freedom in linear model fits >> >> ------------------------------------------------------------------- ------ >> >> Please any help in this regard will be highly appreaciated >> >> >> Rohit >> >> >> >> -- >> Rohit Farmer >> M.Tech Bioinformatics >> Department of Computational Biology and Bioinformatics >> Jacob School of Biengineering and Biotechnology >> Sam Higginbottom Institute of Agriculture, Technology and Sciences >> (Formerly known as Allahabad Agricultural Institute - Deemed University) >> Allahabad, UP, INDIA - 211 007 >> Ph. No. 9839845093, 9415261403 >> e-Mail rohit.farmer at gmail.com >> Blog http://rohitsspace.blogspot.com >> > > > > -- > Rohit Farmer > M.Tech Bioinformatics > Department of Computational Biology and Bioinformatics > Jacob School of Biengineering and Biotechnology > Sam Higginbottom Institute of Agriculture, Technology and Sciences > (Formerly known as Allahabad Agricultural Institute - Deemed University) > Allahabad, UP, INDIA - 211 007 > Ph. No. 9839845093, 9415261403 > e-Mail rohit.farmer at gmail.com > Blog http://rohitsspace.blogspot.com > -- Rohit Farmer M.Tech Bioinformatics Department of Computational Biology and Bioinformatics Jacob School of Biengineering and Biotechnology Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly known as Allahabad Agricultural Institute - Deemed University) Allahabad, UP, INDIA - 211 007 Ph. No. 9839845093, 9415261403 e-Mail rohit.farmer at gmail.com Blog http://rohitsspace.blogspot.com