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Question: High normalized counts on DESeq2 MAplot
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gravatar for rbronste
26 days 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!

ADD COMMENTlink modified 26 days ago by James W. MacDonald48k • written 26 days ago by rbronste60
2
gravatar for Michael Love
26 days ago by
Michael Love20k
United States
Michael Love20k 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 26 days ago by Michael Love20k

Actually I would like to do both. 

ADD REPLYlink written 26 days 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 26 days ago by Michael Love20k

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 26 days ago • written 26 days 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 25 days ago by Michael Love20k

Thanks for the help.

ADD REPLYlink written 25 days ago by rbronste60

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

ADD REPLYlink written 25 days ago by rbronste60
1
gravatar for James W. MacDonald
26 days ago by
United States
James W. MacDonald48k wrote:

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

ADD COMMENTlink written 26 days ago by James W. MacDonald48k
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