Question

Strange MA plot

0

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Yuya Liang ▴ 20

@yuya-liang-14202

Last seen 6.4 years ago

United States

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/

rnaseq deseq2 • 2.1k views

ADD COMMENT • link updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by Yuya Liang ▴ 20

score 0 · Answer 1 · 2017-10-18

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Michael Love 43k

@mikelove

Last seen 8 minutes ago

United States

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 7.2 years ago Michael Love 43k

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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 7.2 years ago Yuya Liang ▴ 20

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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 7.2 years ago Michael Love 43k

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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 7.2 years ago Yuya Liang ▴ 20

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

ADD REPLY • link 7.2 years ago Michael Love 43k

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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="">.

ADD REPLY • link 7.2 years ago Yuya Liang ▴ 20

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You can use DESeq2::plotMA instead of plotMA.

ADD REPLY • link 7.2 years ago Michael Love 43k

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Thank you so much, Dr. Love!!! I got the normal MA plot!

ADD REPLY • link 7.2 years ago Yuya Liang ▴ 20