Entering edit mode
4.6 years ago
swilson
▴
10
I conducted DE analysis using DESeq2, and attempted to sort the top 100 differentially expressed genes (based on their P-values) using the following code:
dds <- DESeq(dds)
res <- results(dds, alpha = 0.05)
resOrdered <- res[order(res$pvalue)]
topGenes <- as.data.frame(res) %>%
tibble::rownames_to_column("GeneID") %>%
arrange(padj) %>%
select
head(100)
topGenes
However, 22 genes have P/Padj- values of zero. Does this make any sense?
Hello, I am now running into zeros as well with about 26 difference genes for padj and pvalues when i run deseq2. Is there a way to extend the number of floating points or should it just be read as extremely small chance due to chance.