Question: Gene set size effect on Gene ontology Semantic Similarity score
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gravatar for ash3m21
3 months ago by
ash3m210
ash3m210 wrote:

Hello everyone,

My name is Ravi and I am a doctoral student studying the biological processes in human ageing. Recently we wanted to also have a bioinformatic analysis of the same. I am trying to understand the effect gene set size has when I am computing the GO semantic similarity score using the R package 'GOSemSim'.

I have a fixed data set containing about 2000 genes, labelled TraitA.

I compute the semantic similarity between TraitA and several other traits, labelled Trait_Random. Trait_Random will have anywhere from 10 to 2000 genes.

How does this difference in gene set size affects the score that I get?

Also is there any statistical method that I could use if there is a bias in the score generated?

Any thoughts or inputs on this would be very helpful. Thank you so much for your time.

ADD COMMENTlink modified 3 months ago by Guangchuang Yu1.4k • written 3 months ago by ash3m210
1
gravatar for Guangchuang Yu
3 months ago by
Guangchuang Yu1.4k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.4k wrote:

should not have bias on gene set size. please refer to the vignette, which describe the calculation in details.

ADD COMMENTlink written 3 months ago by Guangchuang Yu1.4k
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