Question: Problem in Heat map generation of DE genes in Agilent Microarray data analysis
1
gravatar for Vinay Singh
4.3 years ago by
Vinay Singh50
INDIA, New Delhi, JNU
Vinay Singh50 wrote:

Hello to all,

I have started agilent microarray data analysis (one color), I have used R bioconductor for analysis steps i used in are as follows now i am not able to get heatmap of differentially expressed genes . Please help me.

library(limma)

T <-readTargets("Targets.txt")

x <-read.maimages(targets, source="agilent",green.only=TRUE)
y <-backgroundCorrect(x, "normexp", offset=50)
y <-normalizeBetweenArrays(y, method="quantile")

y.ave <- avereps(y, ID=y$genes$ProbeName)

f <- factor(targets$Condition, levels = unique(targets$Condition))

design <- model.matrix(~0 + f)
colnames(design) <- levels(f)

fit <- lmFit(y.ave, design)

contrast.matrix <- makeContrasts("control-drought", "control-heat", "drought-control","control-combined","heat-drought", levels=design)

fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)

C.top<-as.numeric(rownames(topTable(fit2, coef=1,n=50)))

heatmap(y.ave$M[C.top,])
Error in heatmap(y.ave$M[C.top, ]) : 'x' must be a numeric matrix
limma microarray analysis heatmap R • 1.8k views
ADD COMMENTlink modified 20 months ago by RamRS27k • written 4.3 years ago by Vinay Singh50

Hints: what is C.top (it is not defined in the code example),

Your data to give to heatmap must be a numeric matrix (error message is obviously complaining 'it is not'). Output head(y.ave$M[C.top, ]), and you will see what the problem is.

ADD REPLYlink modified 20 months ago by RamRS27k • written 4.3 years ago by Michael Dondrup47k
Sorry I have used this step here before heatmap that is
C.top<-as.numeric(rownames(topTable(fit2, coef=1,n=50)))
ADD REPLYlink written 4.3 years ago by Vinay Singh50

And what about: head(y.ave$M[C.top, ]) ??

ADD REPLYlink modified 20 months ago by RamRS27k • written 4.3 years ago by Michael Dondrup47k

Thanks Michael for paying attention to my problem actually I am a beginner in R I have just referred to the question. Please help me in generating heatmap of DE genes of microarray data.

ADD REPLYlink modified 20 months ago by RamRS27k • written 4.3 years ago by Vinay Singh50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 980 users visited in the last hour