Entering edit mode
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/
Thank you for replying, Sir! The plot I post was the resulting plot when using the code plotMA(). I don't know if it's from DESeq2.
And that's exactly my question. The plot doesn't look like the MA plot from the paper (RNA-seq workflow). I did library DESeq2 package and the same code but the plot came out to my Rstudio was strange.
can you type into the R prompt:
And press Enter. And then reply here what you get? Somehow I think you or someone else has overwritten plotMA in your session.
I got the following output when I typied plotMA in R.
```
> plotMA
function (object, ...)
UseMethod("plotMA")
<environment: namespace:limma>
```
Does it mean I was using limma package to plot? How to change it?
Use DESeq2::plotMA in a session if you’ve loaded limma after DESeq2
You can use DESeq2::plotMA instead of plotMA.
Thank you so much, Dr. Love!!! I got the normal MA plot!