Question: High normalized counts on DESeq2 MAplot
0
gravatar for rbronste
8 months ago by
rbronste60
rbronste60 wrote:

I am wondering how to isolate points on an MAplot that are in the area of high normalized counts above a certain lfc threshold, without changing the low end of the normalized counts that are part of the dds. Also is there a quick way to infer at what alpha these points lie.

Currently Im running the following code and while I do get some of the points in this high count tail, I also get the low. 

resG <- results(dds, lfcThreshold=4, altHypothesis="lessAbs", format = c("DataFrame"), contrast=c("group", "E", "veh"))

drawLines <- function() abline(h=c(-4,4),col="dodgerblue",lwd=2)

plotMA(resG, alpha = .01, ylim = c(-8, 8)); drawLines()

https://www.dropbox.com/s/9og0mhsxrxc2ax9/Screen%20Shot%202018-11-15%20at%202.58.11%20PM.png?dl=0

Thank you!

deseq2 maplot • 201 views
ADD COMMENTlink modified 8 months ago by James W. MacDonald50k • written 8 months ago by rbronste60
Answer: High normalized counts on DESeq2 MAplot
2
gravatar for Michael Love
8 months ago by
Michael Love24k
United States
Michael Love24k wrote:

You want to get the index/rowname of the points or you want to highlight them on the plot? I don't follow your question.

ADD COMMENTlink written 8 months ago by Michael Love24k

Actually I would like to do both. 

ADD REPLYlink written 8 months ago by rbronste60
1

You can use identify() to pick individual points. First do this:

plot(log10(res$baseMean), res$log2FoldChange)

Then you can call identify() with the same two arguments which will let you know the row number of these points. Type Esc to stop the process.

ADD REPLYlink written 8 months ago by Michael Love24k

Very helpful however still confused about the following:

When I do:

plot(log10(res$baseMean), res$log2FoldChange)

​I get now an MA plot that looks like before where every point is a black hollow circle, and if I try to limit it in this way:

plot(log10(res$baseMean > 3), res$log2FoldChange > 0.5)

I get a plot with simply two points.

Maybe Im getting something confused?

​Im just trying to take the red points on the right side of that initial MAplot I posted and isolate them, to see what they are - and wanted to maybe do it without recalling dds with different settings (higher bound on counts).

Also can you apply identify() to plotMA, as in the original one I posted and identify specific points?

ADD REPLYlink modified 8 months ago • written 8 months ago by rbronste60
1

That code above isn’t really a meaningful R expression. The greater than sign is producing a logical vector (0s and 1s...). Maybe follow James advice and just use a built in package, or recruit an R coder to help out.

Yes you can apply identify() to plotMA() output as well. You would take off the log10 from baseMean.

ADD REPLYlink written 8 months ago by Michael Love24k

Thanks for the help.

ADD REPLYlink written 8 months ago by rbronste60

Yes I apologize did not do a simple subset operation there prior to plot. 

ADD REPLYlink written 8 months ago by rbronste60
Answer: High normalized counts on DESeq2 MAplot
1
gravatar for James W. MacDonald
8 months ago by
United States
James W. MacDonald50k wrote:

You might try Glimma, particularly glMDPlot, which is pretty sweet.

ADD COMMENTlink written 8 months ago by James W. MacDonald50k
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