Question: Extract genomic feature related to point from mean-variance plot in limma/voom
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gravatar for James Ashmore
3.4 years ago by
James Ashmore2.7k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.7k wrote:

I am using limma/voom for differential expression analysis and I would like to find out which genomic feature is represented by each point in the mean-variance modelling plot which voom generates. There are some weird trends happening in the data and I'd like to see which genomic features these correspond to. I tried using the save.plot option in the call to voom but it doesn't produce the voom.xy value in the output object?

voom limma • 819 views
ADD COMMENTlink modified 20 months ago by h.mon28k • written 3.4 years ago by James Ashmore2.7k
0
gravatar for h.mon
20 months ago by
h.mon28k
Brazil
h.mon28k wrote:

Old thread, I know, but Biostar bumped it.

With:

v <- voom( x, design, plot = T, save.plot = T )
identify( v$voom.xy, labels = row.names( v ) )

I could click on points and, upon pressing esc, the names of the points clicked were printed on the graph, and their index at row.names( v ) returned. You can also assign the indexes to a variable:

z <- identify( v$voom.xy, labels = row.names( v ) )
z
#[1]  634 3097 4041 9483

rownames(v)[z]
#[1] "C16H1orf115" "POC1A"       "PLPP2"       "FADD"

You also (probably) can accomplish this with the Glimma package, which I never used but seems really great.

ADD COMMENTlink written 20 months ago by h.mon28k
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