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Question: Strange MA plot
0
12 months ago by
United States
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/

modified 12 months ago by Michael Love19k • written 12 months ago by Yuya Liang0
0
12 months ago by
Michael Love19k
United States
Michael Love19k 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?

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:

> plotMA

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

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="">.
1

You can use DESeq2::plotMA instead of plotMA.