[BioC] [topGO] More flexible way to select 'interesting' genes

Enrico Ferrero enricoferrero86 at gmail.com
Wed Aug 7 22:12:40 CEST 2013

Hi Hongxing,

Yes you can, but then you can only perform statistical tests based on
numerical comparisons such as Fisher's test, while you can't use those
that incorporate a ranking of some sort in the analysis, like the KS


On 7 August 2013 21:05, Hongxing Yang <yanghx81 at gmail.com> wrote:
> Hi,
> I think you can directly feed topGO your list of studied genes. Create a
> logical vector for all genes, with the values for wanted genes being TRUE
> and the others FALSE; then set the selection function to select out only
> those TRUE genes.
> cheers
> Hongxing
> 2013/8/7 Enrico Ferrero <enricoferrero86 at gmail.com>
>> Hi,
>> Adrian, I'm using your topGO package and really appreciate how
>> powerful and customizable it is with respect to the choice of
>> algorithms and statistical tests.
>> There's just one limitation that I don't really understand, hopefully
>> you or somebody else in the list can shed some light on this.
>> I usually select 'interesting' genes from gene expression experiments
>> based on two different parameters: their p-value and their
>> log(fold-change).
>> As far as I understand, if I want to run a GO enrichment analysis in
>> topGO using a statistical test that uses ranked gene lists such as KS
>> (Kolmogorov–Smirnov test, also used by GSEA), I can only filter on one
>> paramater (tipically the p-value).
>> This is a consequence of the way the topGOdata objects are built, e.g.:
>> myData <- new("topGOdata", description="myData", ontology="BP",
>> allGenes=myAllGenes, geneSel=geneSelFunc, nodeSize=5, annot=annFUN.db,
>> affyLib="hgu133plus2.db")
>> where:
>> - myAllGenes is a named vector of all p-values for each probe on the
>> array, named after their probeID and
>> - geneSelFunc is a function to select the interesting ones, such as:
>> geneSelFunc <- function (score) {
>>     return(score <= 0.05)
>> }
>> I'm basically looking for a more flexible way to perform the selection
>> of my interesting probes: for example I'd like to only select probes
>> that have a p-value<=0.05 and a |log(fold-change)| >= 1.
>> Is there any way to do this?
>> Thank you.
>> Best,
>> --
>> Enrico Ferrero
>> PhD Student
>> Department of Genetics
>> Cambridge Systems Biology Centre
>> University of Cambridge
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Enrico Ferrero
PhD Student
Steve Russell Lab - Department of Genetics
FlyChip - Cambridge Systems Biology Centre
University of Cambridge

e.ferrero at gen.cam.ac.uk

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