User: Oana VIGY

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Oana VIGY80
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7 years, 1 month ago
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10 years, 1 month ago
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o********@igf.cnrs.fr

Posts by Oana VIGY

<prev • 8 results • page 1 of 1 • next >
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Comment: C: ontoCompare
... Hi Brad, thanks for your explanations and advices. It's meaningful. Best regards, Oana Le 08/08/2012 20:00, Brad Davis a écrit : > Hi Oana, > > I suspect the problem is actually with GO.db rather than goTools. The > problems I ran in to involved GO terms that were either deprecated or ...
written 7.1 years ago by Oana VIGY80
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ontoCompare
... Dear Agnes, I encountered a similar issue last summer (see related messages on the list - August 2011) and exchanged few emails directly with Jean about that (+copy to you). I'm using the "goTools" package in a script which is working fine for few years with the given system : R 2.5.1 and BioCondu ...
go written 7.1 years ago by Oana VIGY80 • updated 7.1 years ago by Brad Davis20
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Comment: C: ontoCompare (goTools) : goidvect error
... Le 04/08/2011 16:03, Vincent Carey a écrit : > there's a clue there: > > look at your data input and see if there is something distinguishing > list(goAnnotation)[6797] from list(goAnnotation)[6796] Within that input file, the highlighted GO term is GO:0030165.**If I run the program on ...
written 8.1 years ago by Oana VIGY80
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Comment: C: ontoCompare (goTools) : goidvect error
... I set the option and I obtain the following after half hour: Starting ontoCompare... Error in goidvect[test] : invalid subscript type 'list' Enter a frame number, or 0 to exit 1: ontoCompare(list(goAnnotation), probeType = "GO", method = "TIDS", goType = 2: lapply(tmp, parentsVectWraper, endnode) ...
written 8.1 years ago by Oana VIGY80
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Answer: A: ontoCompare (goTools) : goidvect error
... Hi All, thanks for your replies. I've just finished few more tests on an up-to-date R and BioConductor as Robert suggested (R 2.13 and goTools 1.26.0). My original test file contains 7000 GO terms (can be sent) and it fails after 25 minutes. /Starting ontoCompare... Error in goidvect[test] : inva ...
written 8.1 years ago by Oana VIGY80
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Comment: C: ontoCompare (goTools) : goidvect error
... Hi Robert, it's the contrary : the script still works with the old R and BioConductor but not with the current release versions... that's why I keep the old ones. So, if I could upgrade with a working script, that would be great. Best regards, Oana Le 03/08/2011 21:57, Robert Gentleman a écrit ...
written 8.1 years ago by Oana VIGY80
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ontoCompare (goTools) : goidvect error
... Dear All, I'm using the "goTools" package in a script which is working fine for few years with the given system : R 2.5.1 and BioConductor 2.0.8. In 2009, I tried to upgrade BioConductor and R but I encountered time-consuming problems as others on the list (1st message by Scott Markel, 11/06/2009) ...
go gotools written 8.1 years ago by Oana VIGY80
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question about ontoCompare() performance change
... Dear All, I notice the same problem of time-consuming. Hopping the problem will be resolved soon. Best regards, Oana Jean-Pierre Desvignes a ?crit : > Hello, > > I have the same problem as Scott. When I compared 2 lists of go term (1000 > values for the first list and 4000 for the se ...
go process gotools written 10.1 years ago by Oana VIGY80

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