Pablo Andretta Jaskowiak | 5 Oct 23:20 2012
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GOSim Problem

I'm trying to calculate gene similarities for the yeast organism, but no
matter which ontology or which term similarity I employ I get a lot of
zeros in the gene similarity matrix. In fact the vast majority of the
similarities turn out to be zero. Is this normal?

I'm employing GOSim as in the following:

library('org.Sc.sgd.db')

library('GOSim')

setEvidenceLevel(evidences = "all", organism=org.Sc.sgdORGANISM,
gomap=org.Sc.sgdGO)

setOntology(ont='MF')

getGeneSim(as.character(labels),similarityTerm='Resnik')

My vector named labels, contain gene names such as: YAL003W YAL004W YAL005C
YAL008W YAL010C YAL011W YAL016W YAL018C.

The result for such example are:

 YAL003W    YAL005C YAL008W YAL010C YAL011W   YAL016W YAL018C

YAL003W 1.00000000 0.06968198       0       0       0 0.0588447       0

YAL005C 0.06968198 1.00000000       0       0       0 0.3116553       0

YAL008W 0.00000000 0.00000000       1       0       0 0.0000000       0

YAL010C 0.00000000 0.00000000       0       1       0 0.0000000       0

YAL011W 0.00000000 0.00000000       0       0       1 0.0000000       0

YAL016W 0.05884470 0.31165527       0       0       0 1.0000000       0

YAL018C 0.00000000 0.00000000       0       0       0 0.0000000       1

Is this amount of zeros normal?

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