search for: makecontrasts

Displaying 10 results from an estimated 10 matches for "makecontrasts".

2006 Dec 17
2
question
...aris, France library(marray) library(limma) ....... Rawdata <- read.GenePix(targets=Macro_Mono_targets,skip=107) design<- cbind(individual=c(0,0,1,1,2,2,3,3,4,4,5,5), dim1=c(1,0,1,0,1,0,1,0,1,0,1,0),dim2=c(0,1,0,1,0,1,0,1,0,1,0,1)) fit <- lmFit(normdata@maM, design) contrast.matrix<-makeContrasts(dim1vsdim2=dim2-dim1, levels=design) fit2 <- contrasts.fit(fit,contrast.matrix) fiteb <- eBayes(fit2) Toptable <- topTable(fiteb,number = 10600,genelist=maGeneTable(normdata), sort.by="P", resort.by= "M", adjust="BY") write.table(Toptable,file="RNG_Best_1...
2011 Nov 22
2
filtering probesets with Bioconductor?
...n to approach this? I have looked into using the genefilter() function but can't figure out if it can take the right parameters (i.e. specific probe set id's). Thanks in advance, -M This is the code I used to generate my topTable > fit <- lmFit(eset, design) > cont.matrix <- makeContrasts(NormalvsTumor=Tumor-Normal, levels=design) > fit2 <- contrasts.fit(fit, cont.matrix) > fit2 <- eBayes(fit2) > topTable(fit2, number=100, adjust="BH") -- View this message in context: http://r.789695.n4.nabble.com/filtering-probesets-with-Bioconductor-tp4097747p4097747.htm...
2004 Dec 20
2
problems with limma
...; ts <- c(1,1,1,2,2,2,3,3,3,4,4,4) > ts <- as.factor(ts) > levels(ts) <- c("nzwC","nzwT","akrC","akrT") > design <- model.matrix(~0+ts) > colnames(design) <- levels(ts) > fit4 <- lmFit(all,design) > cont.matrix <- makeContrasts( + Baseline = akrC - nzwC, + NZW_Smk = nzwT - nzwC, + AKR_Smk = akrT - akrC, + Diff = (akrT - akrC) - (nzwT - nzwC), + levels=design) > fit42 <- contrasts.fit(fit4,cont.matrix) > fit42 <- eBayes(fit42) > # > topTable(fit42,coef="Baseline",a...
2010 Mar 29
1
stuck with affy / limma
...[sel, ], labRow=u) ### in this case it works to extract the gene symbol ### limma contrasts design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3))) colnames(design) <- c("control", "three", "six") fit <- lmFit(x, design) meanSdPlot(x) contrast.matrix <- makeContrasts(three-control, six-control, levels=design) fit2 <- contrasts.fit(fit, contrast.matrix) fit2 <- eBayes(fit2) #### top list topTable(fit2, coef=1, adjust="BH", number=20, sort.by="M") library(hgu133plus2.db) u<-mget(row.names(fit2),hgu133plus2SYMBOL) How can I produce a...
2007 Nov 13
0
need help with error message:Error in lm.fit(design, t(M)) : incompatible dimensions
...ot;contrasts") attr(,"contrasts")$f [1] "contr.treatment" colnames(design)<- c("A_xen", "B_crp") # Define colnames of the design matrix fit<-lmFit(xen1dataeset,design) # Fit linear model based on the design matrix contrast.matrix<- makeContrasts(B_crp- A_xen) # define contrast matrix fit2<-contrasts.fit(fit,contrast.matrix) # calculate contrast fit3<-eBayes(fit2) # Calculate B and P-values for contrast crpMxen<-topTable(fit3,coef=1,number=22690,adjust.method="BH",sort.by='B') [[alternative...
2012 May 04
0
LIMMA decideTests result zero from contrast matrix
...a) > samples <- c("Un","Un","DMSO10","DMSO10","DMSO5","DMSO5"); > fl <- as.factor(samples) > design <- model.matrix(~ 0+ fl) > colnames(design) <- levels(fl) > fit <- lmFit(eset, design) > cont.matrix <- makeContrasts(DMSO10-Un, DMSO5-Un, levels=design) > fit2 <- contrasts.fit(fit, cont.matrix) > fit2 <- eBayes(fit2) > tTUni<- topTable(fitUni, adjust="fdr", sort.by="B", number=numGenes) > results <- decideTests(fit2) > vennDiagram(results,include=c("up",&q...
2004 Dec 21
0
Fwd: problems with limma
...2,3,3,3,4,4,4) >> ts <- as.factor(ts) >> levels(ts) <- c("nzwC","nzwT","akrC","akrT") >> design <- model.matrix(~0+ts) >> colnames(design) <- levels(ts) >> fit4 <- lmFit(all,design) >> cont.matrix <- makeContrasts( > + Baseline = akrC - nzwC, > + NZW_Smk = nzwT - nzwC, > + AKR_Smk = akrT - akrC, > + Diff = (akrT - akrC) - (nzwT - nzwC), > + levels=design) >> fit42 <- contrasts.fit(fit4,cont.matrix) >> fit42 <- eBayes(fit42) >> # >> t...
2009 Feb 12
0
Error Message: Error in dim(data) <- dim : attempt to set an attribute on NULL
...e following design <- model.matrix(~0+TS) #write design object to text file write.table(design,file="design.txt",sep="\t",col.names=NA) colnames(design) <- levels(TS) #for eset put in your M values - see ?lmFit for object types fit <- lmFit(eSet, design) cont.matrix<-makeContrasts(s0vss24=s.0-s.24, s24vss48=s.24-s.48, s48vss96=s.48-s.96, c0vsc24=c.0-c.24, c24vsc48=c.24-c.48, c48vsc96=c.48-c.96, levels=design) write.table(cont.matrix,file="cont.matrix.txt",sep="\t",col.names=NA) # estimate the contrasts and put in fit2 fit2 <- contrasts.fit(fit, cont.ma...
2007 Aug 03
4
FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
...; Data<-ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) > ##normalisation > eset.rma<-rma(Data) > ##analysis > targs<-factor(pData(pd)$Target) > design<-model.matrix(~0+targs) > colnames(design)<-levels(targs) > fit<-lmFit(eset.rma,design) > cont.wt<-makeContrasts("treatment1-control","treatment2-control",level > s= > design) > fit2<-contrasts.fit(fit,cont.wt) > fit2.eb<-eBayes(fit2) > testconts<-classifyTestsF(fit2.eb,p.value=0.01) > topTable(fit2.eb,coef=2,n=300) > topTable(fit2.eb,coef=1,n=300) > >...
2007 Jul 30
0
problems in limma
...start, tol = tol, maxit = maxit, trace = trace) 2: Too much damping - convergence tolerance not achievable in: glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace = trace) > fitMA.pi<-lmFit(MA.p[i,],design,ndups=2,correlation=corMA.pi$consensus.correlation) contrast.matrix<-makeContrasts(plain,plateau-PLATEAU,PLATEAU,levels=design) contrast.matrix Contrasts Levels plain plateau - PLATEAU PLATEAU plain 1 0 0 plateau 0 1 0 PLATEAU 0 -1 1 > colnames(contrast.matrix)<-cbind("plai...