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Question: Strange MA plot
0
gravatar for Yuya Liang
4 weeks ago by
Yuya Liang0
Texas, USA
Yuya Liang0 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/

 

ADD COMMENTlink modified 4 weeks ago by Michael Love14k • written 4 weeks ago by Yuya Liang0
0
gravatar for Michael Love
4 weeks ago by
Michael Love14k
United States
Michael Love14k 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 COMMENTlink written 4 weeks ago by Michael Love14k

  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 REPLYlink modified 4 weeks ago • written 4 weeks ago by Yuya Liang0

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 REPLYlink written 4 weeks ago by Michael Love14k

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 REPLYlink written 4 weeks ago by Yuya Liang0

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

ADD REPLYlink written 4 weeks ago by Michael Love14k
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 REPLYlink written 4 weeks ago by Yuya Liang0
1

You can use DESeq2::plotMA instead of plotMA.

ADD REPLYlink written 4 weeks ago by Michael Love14k

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

ADD REPLYlink written 4 weeks ago by Yuya Liang0
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