Hello,

So, I tried to analyze RNA-seq data using Limma. I have done the workflow like this, starting from reading the read count from files. For the samples, there are 3 samples of group 1 and 7 samples of group 2.

readCountClean <- read.table("MergedGeneCountCleaned.csv",header=TRUE,sep=",",row.names=1)
dgeList<-DGEList(readCountClean)
dgeList<-calcNormFactors(dgeList)
designVoom <- matrix(c(rep(1,3),rep(0,7),rep(0,3),rep(1,7)),ncol=2)
vRnaSeq <- voom(dgeList,designVoom,plot=TRUE)

rnaSeqFit <- lmFit(vRnaSeq,designVoom)
rnaSeqFit <- ebayes(rnaSeqFit)

rnaSeqDEGenes <- topTable(rnaSeqFit, coef=2)

The topTable gives error because rnaSeqFit after ebayes function is not MArrayLM object even though I got MArrayLM after the lmFit function. It means the error is during ebayes. Also, from the size of the data, the output of ebayes is far smaller than after the lmFit function. What is the cause of it?

Use eBayes, not ebayes. They are different functions; the latter is an internal function that is not meant to be called directly, but is instead called within the former (which is what you should be using).