Hi guys, I have an issue... I'm doing some analysis using DESEq2. By default I know that when I create the object dds using
dds <- DESeqDataSetFromMatrix(countData = count.table, colData = data.frame(treatment=treatment), design = ~ treatment)
an as treatment (control vs recurrence) by default R R will choose as reference level the factors based on alphabetical order, so in this case, the reference level would be control. But I have a question about this, for the downstream analysis, when I run for example:
dds <- DESeq(dds) res <- results(dds) res2Order <-res2[order(res2$pvalue), ] write.table(res2Order, file="my _table")
I assume that the genes reported in my table with p-value < 0.05 are deferentially expressed in cotrol vs. recurred, but does it means that they are more or less expressed in control than recurred, but how can I know if this difference is based on a higher or lower expression? For example,can I confirm that a gene with p-value < 0.05 is more expressed in control than recurrence?
Many thanks in advance!