I'm looking into the differentially expressed genes in heat-stressed animals versus normal ones.
When I only done the analysis on the 6 samples (3 heat stressed and 3 non-stressed) I got a few significant genes that are significantly differentially expressed on stress.
When I did the DEseq analysis using data matrix of all samples that include RNA-seq of 40 samples 3 of them are heat stressed the other 3 are non-stressed and the rest are of different other conditions like ageing and cold stress.
dds <- DESeqDataSetFromMatrix(countData = data, colData = samples, design = ~0+condition) and in my DEseq contrast ageing <- results(dds_lrt, contrast = c("condition", "5.months.old", "young")) stressed <- results(dds_lrt, contrast = c("condition", "heat-stressed", "control"))
by applying that I got hundreds of significant genes.
Is this a right way of doing it and the volcano blot is weird