User: Ariel Chernomoretz

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Posts by Ariel Chernomoretz

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genomicAlignments: fail to run readGAlignments example code
... Hi I got an error message when trying to read bam files (genomicAlignments 1.10). I even got this error when trying to run the provided examples. Follows: example code, traceback and sessionInfo Thanks in advance for any help. Ariel   > example(readGAlignments) rdGAlg> ## ------------- ...
genomicalignments written 2.9 years ago by Ariel Chernomoretz160 • updated 2.9 years ago by Valerie Obenchain6.7k
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Comment: C: frma vectors for mouse 430 2.0
... Thanks from your prompt answer Matt, I realized that the frma vignette does mention that mouse4302 is supported! (my fault!) Best Ariel./ PS: perhaps you could expand the frma suggested package information to include mouse4302 ...just to improve visibility On Wed, Jun 22, 2011 at 12:42 PM, Matthew ...
written 8.5 years ago by Ariel Chernomoretz160
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frma vectors for mouse 430 2.0
... Hi Matt, and BioCs I am about to start an analysis of a manually curated dataset built upon ~80 GDS's (Mouse 430 2.0 platform) I wonder if there are plans to support that platform in near-future releases of frma. Thanks in advance Ariel./ Dr. Ariel Chernomoretz Integrative Systems Biology Group Fun ...
frma written 8.5 years ago by Ariel Chernomoretz160 • updated 8.5 years ago by Matthew McCall830
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Comment: C: how to unlock a package environment
... Excelent news... (I noticed that there is an 'org.At.tair.db' also available in the devel version!) Thanks Herve for the info A./ PS: I am still curious about the locking/unlocking issue... 2009/10/1 Hervé Pagès > Forgot to send my sessionInfo(), sorry: > > > sessionInfo() > R ...
written 10.2 years ago by Ariel Chernomoretz160
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how to unlock a package environment
... Hi all, I am currently analyzing some arabidopsis thaliana experiments (ath1121501 GeneChip) The corresponding annotation package, ath1121501.db, is a little bit 'special' as there is no ENTREZID map for the chip. I would like to cheat and create a fake ath1121501ENTREZID for the environment as a c ...
annotation arabidopsis thaliana ath1121501 genefilter written 10.2 years ago by Ariel Chernomoretz160 • updated 10.2 years ago by Marc Carlson7.2k
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How to use the same node layout for a set of graph plots using graph and Rgraphviz?
... Hi Hugh, I was testing your handy code and got the following weird behavior. For some input graphs plotGraphWithTemplate works fine with the default layout ("dot") but fails when "neato" is requested. Of course this has to do more with the Rgraphviz plot call rather than with your function , but I ...
rgraphviz written 11.8 years ago by Ariel Chernomoretz160 • updated 11.8 years ago by Rand, Hugh50
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Comment: C: Rgraphviz, deprecated imageMap
... Thanks! a./ On Nov 26, 2007 4:07 PM, Herve Pages wrote: > Hi Ariel, > > Ariel Chernomoretz wrote: > > Hi Robert, > > > > Thanks for your quick answer. > > The problem is that Rgraphviz sets in fact a new method to > > the generic function 'imageMap' from gene ...
written 12.0 years ago by Ariel Chernomoretz160
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Comment: C: Rgraphviz, deprecated imageMap
... Hi Robert, Thanks for your quick answer. The problem is that Rgraphviz sets in fact a new method to the generic function 'imageMap' from geneplotter, that accept an Ragraph object (and not a matrix with boxplot coordinates) as the first argument . Regards Ariel./ On Nov 26, 2007 1:32 PM, Robert G ...
written 12.0 years ago by Ariel Chernomoretz160
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Rgraphviz, deprecated imageMap
... Hi BioC's and Rgraphviz maintainers, I have recently installed BioC 2.1 on R 2.6 and I found that the imageMap function is not included anymore in Rgraphviz 1.16. I found that function real handy to produce visual reports of GO overrepresentation analysis performed mainly with GOstats. (As a matter ...
rgraphviz process gostats written 12.0 years ago by Ariel Chernomoretz160 • updated 12.1 years ago by rgentleman5.5k
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go count
... hi all, is there a simple way to calculate how many entrez id's are mapped to a given GO node for for a given species? thanks ariel./ ...
go written 12.4 years ago by Ariel Chernomoretz160 • updated 12.4 years ago by Seth Falcon7.4k

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