Hi Lorraine/folks I have previously managed to use DegPlot as you have know. However, just now when I run similar chunk, it gives me the output of - which I have trouble interpreting what it means. my goal is to see how the top genes varies across all my sample groups Could you give me a clue? thanks
Error in `$<-.data.frame`(`*tmp*`, "xs", value = integer(0)) : replacement has 0 rows, data has 96
The chunk that was ran (it was a 2x2 factorial):
dds <- DESeqDataSet(gse, design = ~ gender*treatment)
dds <- DESeq(dds)
res<-results(dds)
degPlot(dds, res=res, n=10, xs = "group",group="group",groupLab = "sampletype",ann = c("gene_id","symbol"),color="Accent")
Intuitively, i think it has something to do with the group variable. However, I was wondering if the group variable is automatically extracted/defined from the dds/res? thanks
thanks Kevin managed to resolve it with your suggestions