Hi everyone,
I got a strange MA plot like this:
The code I used was simply like the manual:
lncap_de <- DESeq(data_deseq_1)
lncap_de_out <- results(lncap_de)
res <- results(lncap_de, alpha = 0.05)
plotMA(res)
And, I checked the result by: head(res[ order(resSig$log2FoldChange), ])
It looks like (log2FoldChange seems normal):
Does anyone know the reason and how to fix it?
I tried demo data from DESeq and got the same strange MA plot as well.
dds <- makeExampleDESeqDataSet()
dds <- DESeq(dds)
res <- results(dds)
plotMA(res)
I run R version 3.4.0 (2017-04-21) on Platform: x86_64-apple-darwin15.6.0 (64-bit) under: macOS Sierra 10.12.6, with DESeq2_1.16.1
Thank you in advance! Sorry for messy message. For more detail about my question: https://www.biostars.org/p/278326/

