Question: limma barcodeplot(): calculation of enrichment score
1
gravatar for khandarius
7 months ago by
khandarius20
khandarius20 wrote:

Hello,

 

I've performed gene set enrichment analysis with the limma-package's camera -function. I'm using limma's barcodeplot -function to visualize my results (one index set, no gene weights). I would like to know how the enrichment score on the plot (y-axis) is calculated - I can't find any mention of it in the help files or limma's user guide. An example of a barcode plot can be found here (figure 9): https://f1000research.com/articles/5-1438/v2.

 

Best regards,

Darius

ADD COMMENTlink modified 7 months ago by Aaron Lun23k • written 7 months ago by khandarius20
Answer: limma barcodeplot(): calculation of enrichment score
2
gravatar for Aaron Lun
7 months ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

It's done using the function tricubeMovingAverage, with the span defined with span.worm. Imagine a sliding window that is applied to the set of all genes (ordered by log-fold change for your contrast of interest). In each window, you calculate the "density" of genes in the specified gene set, where the contribution of each gene in the window is weighted according to its distance from the center. The computed value for each position of the window is the enrichment score. I would say that it's mostly for visual purposes and should not be used for any quantitative decision-making.

ADD COMMENTlink written 7 months ago by Aaron Lun23k
1

See also How barcode-plot enrichment is calculated?

ADD REPLYlink written 7 months ago by Gordon Smyth37k

Thank you Gordon. I don't know how I missed this post...

ADD REPLYlink written 7 months ago by khandarius20
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