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...