Hi,
I want to set the p-value and LFC threshold to DESeq2 output results
The way i understood is
independentFiltering = TRUE,alpha = 0.001 #will filter results for p-value 0.001.
However, how to set an LFC threshold of 1.5. Is it lfcThreshold = 1.5?
Also, how to identify upregulated and downregulated genes.
The summary list by the p-value of DESeq2 run is as follows
res <- res[order(res$padj),]
head(res)
In this, I assume the genes with negative LFC are downregulated. But in which group LD1 or control?
Thank you for the help