Error while running Limma
0
0
Entering edit mode
7 weeks ago

I'm stuck while running the limma at design matrix step. It showing error stating that "Error in lmFit(LIMS, design.gse74706):row dimension of design doesn't match column dimension of data object". This is my code for running limma.

Col_data = read.table(file = "LUSC_Phenotype.txt", header = T, sep = "\t")
groups.LUSC = Col_data$Type
f.LUSC = factor(groups.LUSC, levels=c("Tumor", "Normal"))
design.LUSC = model.matrix(~0+f.LUSC)
colnames(design.LUSC) = c("Tumor", "Normal")
LIMS <- read.delim(file.choose(), row.names=1)
data.fit.LUSC = lmFit(LIMS, design.LUSC)
contrast.matrix.LUSC = makeContrasts(Tumor-Normal, levels=design.LUSC)
data.fit.con.LUSC = contrasts.fit(data.fit.LUSC, contrast.matrix.LUSC)
data.fit.eb.LUSC = eBayes(data.fit.con.LUSC) 
Microarray Limma Design matrix • 174 views
ADD COMMENT
0
Entering edit mode

the error is saying that the number of columns in LIMS doesn't match the number of rows in design.LUSC. Can you confirm that LIMS is formatted with genes as rows and samples as columns (i.e. a standard "gene count matrix")? Likewise double check the design.LUSC object is as you expect.

ADD REPLY

Login before adding your answer.

Traffic: 1121 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6