Strange MA plot

Question: Strange MA plot

12 months ago by

Yuya Liang • 0

United States

Yuya Liang • 0 wrote:

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/

deseq2 rnaseq

ADD COMMENT • link •

modified 12 months ago by Michael Love ♦ 19k • written 12 months ago by Yuya Liang • 0

12 months ago by

Michael Love ♦ 19k

United States

Michael Love ♦ 19k wrote:

That isn’t DESeq2’s plotMA function, I can tell by styling. Are you saying the plotMA function from DESeq2 looks similar to that one?

ADD COMMENT • link written 12 months ago by Michael Love ♦ 19k

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.

ADD REPLY • link modified 12 months ago • written 12 months ago by Yuya Liang • 0

can you type into the R prompt:

> plotMA

And press Enter. And then reply here what you get? Somehow I think you or someone else has overwritten plotMA in your session.

ADD REPLY • link written 12 months ago by Michael Love ♦ 19k

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?

ADD REPLY • link written 12 months ago by Yuya Liang • 0

Use DESeq2::plotMA in a session if you’ve loaded limma after DESeq2

ADD REPLY • link written 12 months ago by Michael Love ♦ 19k

I'm not sure if I did correct. I typed DESeq2::plotMA and checked `plotMA` my environment still shows <environment: namespace:limma="">. After that, I unloaded limma package by clicking "package" icon from right part of Rstudio but still got strang MA plot. The environment still <environment: namespace:limma="">.

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