Error while running Limma

Question

[prithvi.mastermind]

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) 

[jv]

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.