User: Paolo Sonego

gravatar for Paolo Sonego
Paolo Sonego140
Reputation:
140
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Location:
Italy
Last seen:
6 years, 9 months ago
Joined:
9 years, 6 months ago
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p***********@gmail.com

Posts by Paolo Sonego

<prev • 14 results • page 1 of 2 • next >
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Problem installing KEGGSOAP
... Hi, I'm trying to install KEGGSOAP on a Mac (MAC OS X 10.5.8) but I get this error: Error : .onLoad failed in loadNamespace() for 'KEGGSOAP', details: call: validObject(.Object) error: invalid class “WSDLMethod” object: undefined class for slot "returnValue" ("GenericSchemaType") Error: packa ...
keggsoap written 6.8 years ago by Paolo Sonego140 • updated 6.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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Visualising the GO structure (RNA-seq) using topGO, and goseq
... Dear Marc, Thanks for the answer! I'll take a look at the suggested vignette (I read it long ago and I forgot Occam's razor) and see if I can adapt the described procedure to my pipeline. Regards, Paolo Message: 17 Date: Tue, 29 Mar 2011 16:53:05 -0700 From: Marc Carlson To: bioconductor@r-project. ...
microarray go visualization graph topgo goseq written 7.4 years ago by Paolo Sonego140
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Visualising the GO structure (RNA-seq) using topGO and goseq
... Hi all, I'd like to investigate how significant GO terms are distributed over the GO graph for RNA-seq differentially expressed genes checked for over-reppresentation using the procedure available in the goseq package. The topGO package (see, for example, the chapter 7.4 of the included vignette) a ...
microarray go visualization written 7.4 years ago by Paolo Sonego140 • updated 7.4 years ago by Marc Carlson7.2k
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Comment: C: Processing of Illumina Infinium methylation microarray data using lumi - addColo
... Dear Sean, Thanks for the quick and effective solution! My problem was I previously installed the IlluminaHumanMethylation27k.db using the standard procedure: > source("http://bioconductor.org/biocLite.R") > biocLite("IlluminaHumanMethylation27k.db") Unfortunately on the release rep ...
written 7.8 years ago by Paolo Sonego140
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Processing of Illumina Infinium methylation microarray data using lumi - addColorChannelInfo bug?
... Hi guys, I'm trying to analyze some Illumina Infinium methylation microarray data using the new lumi package (btw, great improvement and nice brand new methylation vignette). The following error is produced when trying to replicate the example in the addColorChannelInfo() manual > ?addColorChan ...
lumi written 7.8 years ago by Paolo Sonego140 • updated 7.8 years ago by Sean Davis21k
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KEGGSOAP package: I can't retrieve KEGG pathway diagrams
... Dear all, I need to retrieve a KEGG pathway diagram using the KEGGSOAP package. Until now it always works (time ago, thanks to the list, I solved a proxy problem to tell the full story). To check my environment I c & p an example from the color.pathway.by.objects function help page: ...
hgu133a keggsoap written 9.1 years ago by Paolo Sonego140
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Comment: C: EBImage problem - requested image not found or could not be loaded
... Dear Gregoire, Thanks so much! Thanks to your suggestions my admin managed to solve the problem! It seems, if I understand correctly, that under gentoo the default installation of ImageMagick doesn't include libXML support. Emerging(gentoo-lingo to mean install, i guess) the ImageMagick package wi ...
written 9.3 years ago by Paolo Sonego140
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EBImage problem - requested image not found or could not be loaded
... Dear all, Solved one problem and got another :'( I'm trying to use EBImage to read a gif image at a specific url. My commands: > library(KEGGSOAP) > url.gif <- color.pathway.by.objects("path:eco00260", + c("eco:b0002", "eco:c00263"), + ...
ebimage written 9.3 years ago by Paolo Sonego140 • updated 9.3 years ago by Gregoire Pau310
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Comment: C: KEGGSOAP (installation?) problem
... Dear Marc, Thanks for the quick reply. My admin solved the problem: it was a proxy issue! TFYT! Regards, Paolo ...
written 9.3 years ago by Paolo Sonego140
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KEGGSOAP (installation?) problem
... Dear all, I'm not sure if this could be considered a bug... I need to use the KEGGSOAP package to retrieve some KEGG pathway diagrams. Below is the procedure I followed to check the KEGGSOAP package: library(KEGGSOAP) ## from the mark.pathway.by.objects help page > url <- color.pathway.by ...
keggsoap written 9.3 years ago by Paolo Sonego140 • updated 9.3 years ago by Marc Carlson7.2k

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