User: Jesper Ryge

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Jesper Ryge110
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Posts by Jesper Ryge

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Answer: A: error installing R 2.9.1 from source on mac os 10.5?
... thanx:-) solved it. was a stupid issue, part of the path to the R folder from which the installation was performed contained a space, like "user/install folder/R-2.9.0" which apparently it could not handle... now its running... jesper Ryge ----- Original Message ----- From: Patrick Aboyoun Dat ...
written 9.8 years ago by Jesper Ryge110
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error installing R 2.9.1 from source on mac os 10.5?
... hi i get an error when trying to install R 2.9.1 from source on an intel mac os 10.5.7. i have used the gcc4.2 from xcode 3.1 and gfortran 4.2 from http://r.research.att.com/tools/. i also tried using gcc and gfortran 4.3 installed with macports. same error. im not an expert in this and im a bit lo ...
written 9.8 years ago by Jesper Ryge110
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Comment: C: biomaRt and Ensembl probe set filter....
... hi james ----- Original Message ----- From: Cei Abreu-Goodger Date: Monday, January 26, 2009 3:24 pm Subject: Re: [BioC] biomaRt and Ensembl probe set filter.... To: "James W. MacDonald" Cc: Jesper.Ryge at ki.se, bioC > > > James W. MacDonald wrote: > > HI Jesper, > > > ...
written 10.3 years ago by Jesper Ryge110
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Comment: C: biomaRt and Ensembl probe set filter....
... hi jim thanx for the fast answer:-) still small bumps on the way but getting better.... installed biomaRt_1.16.0 and now i can run: mart <- useMart("ensembl_mart_47", dataset="rnorvegicus_gene_ensembl",archive=T) also for ensembl_mart_46, but not for mart_45 and downwards... even thought the ...
written 10.3 years ago by Jesper Ryge110
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biomaRt and Ensembl probe set filter....
... Hi everybody q1. I have been using biomaRt to filter Affymetrix probe sets prior to statistical testing such as limma or cyberT. That is, I only include probe sets that are annotated in ensembl. In this sense I get rid of probe set that do not align correctly to the intended genes - at least that ...
cdf probe affy graph limma biomart written 10.3 years ago by Jesper Ryge110 • updated 10.3 years ago by James W. MacDonald50k
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Comment: C: Biomart mysql error...
... thanx laurent :-) ----- Original Message ----- From: Laurent Gautier Date: Monday, December 1, 2008 7:16 pm Subject: Re: [BioC] Biomart mysql error... To: Jesper.Ryge at ki.se Cc: "bioconductor mail list bioconductor at stat.math.ethz.ch" > > The issue is likely on the server end (updates ...
written 10.5 years ago by Jesper Ryge110
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Biomart mysql error...
... Hi im running into a biomaRt problem when i use the mysql=T in useMart which has worked very well earlier on my computer (MacPro3,1 )??? Here is a short illustration: > library(biomaRt) > mart <- useMart("ensembl" ,dataset="rnorvegicus_gene_ensembl",mysql=T) connected to: ensembl Read ...
biomart written 10.5 years ago by Jesper Ryge110 • updated 10.5 years ago by laurent140
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Comment: C: GOstats, geneCounts and gene universe filtering...
... its works:-) one more question regarding GOstats.-) in ur description of the GOstats package u mention that the conditional test is similar to that presented in alexa et al 2006. would that be like the elim or weight function they describe? i tried compare GOstats and topGO (alexa GO analysis pack ...
written 12.0 years ago by Jesper Ryge110
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Comment: C: GOstats, geneCounts and gene universe filtering...
... thanks for the fast answer:-) its nice to know im battling my way in the right direction... here is the session info u requested (im using a mac powerPC G4 with mac Os 10.4.9 if thats of any help...) : > sessionInfo() R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1 locale: C attached ...
written 12.0 years ago by Jesper Ryge110
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GOstats, geneCounts and gene universe filtering...
... Hi, Im trying to perform an enrichment analysis for GO terms on my microarray results. my problem arises when i noticed that the geneCount(x) doesnt match the amount of genes annotated at certain nodes using geneIdsByCategory(x). maybe thats ok, i just wondered if that is actually ok or if i misse ...
go rat2302 probe gostats topgo written 12.0 years ago by Jesper Ryge110 • updated 12.0 years ago by Seth Falcon7.4k

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