I'm looking for the differential gene expression in a somatic embryogenesis process. The thing is that i need to compare 5 conditions (stages) versus "control", each condition with two replicates. My question is... can i compare all in one run or do i need to compare by pares? And... how can i manage the replicates?
I started creating a count matrix (with data from the htseq count) comparing one condition versus control (with the 2 replicates of each one), and this command line:
countsTable <- read.csv("controlvs9.csv", header=F, sep="\t")
colData = data.frame(condition = factor(c( "control", "control", "9days", "9days")))
dds <- DESeqDataSetFromMatrix(countData=countsTable, colData = colData, design=~condition))
and i get the results in 4 columns (because of the replicates", but i dont know if this is ok. i was expecting to get only two: control and 9days.
and also... i can't asign the first column which contains the names of the genes.
hope someone can help me