Closed:DESeq2 for two file.BAM

Question

[Morris_Chair]

Hi,

I am new to RNAseq and shortly I will receive the raw files of my experiment. So far I found very helpful this forum where I found lots of helpfull information but now I have "rare" question.

I'm trying to make plots by precticing with two BAM files from a set of a large experiment.. My question is, if I want to compare this two samples, and I want to see what genes are differentially expressed without using any replicate, is that possible?

Here is the command line used with Rstudio and the error that I gets

library("DESeq2")

countdata <- as.matrix(read.table("DESeq2_STAR/counts.table", header=TRUE, row.names = 1))
condition <- factor(c(rep("CUTLL1", 1), rep("KOPTK1", 1)))
coldata <- data.frame(row.names=colnames(countdata), condition)
dds <- DESeqDataSetFromMatrix(countdata, coldata, design=~condition)
dds$condition <- relevel(dds$condition, ref="CUTLL1")
dds <- DESeq(dds)


**estimating size factors
estimating dispersions

Error in checkForExperimentalReplicates(object, modelMatrix) :

The design matrix has the same number of samples and coefficients to fit,

so estimation of dispersion is not possible. Treating samples

as replicates was deprecated in v1.20 and no longer supported since v1.22.**

Thank you for help :)