Hi All
I am trying to choose between the following:
a) using all the genes in my genome as a background for my GO analysis
or
b) using only those genes that have at least 1 GO term as a background for my GO analysis
Option a) gives me more (32) enriched GO terms when compared to a set of differentially expressed genes and enhanced q-values
option b) gives me less (18) enriched GO terms when compared to a set of differentially expressed genes and relatively higher q-values than option a.
Any help is appreciated. FYI, I am using GOSEQ for my analysis.
I am trying to choose between the following:
a) using all the genes in my genome as a background for my GO analysis
or
b) using only those genes that have at least 1 GO term as a background for my GO analysis
Option a) gives me more (32) enriched GO terms when compared to a set of differentially expressed genes and enhanced q-values
option b) gives me less (18) enriched GO terms when compared to a set of differentially expressed genes and relatively higher q-values than option a.
Any help is appreciated. FYI, I am using GOSEQ for my analysis.
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