Question: GOstats and library ath1121501
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gravatar for Martin Olivier
13.1 years ago by
Martin Olivier70 wrote:
Hello, I don't know very well the bioconductor packages, but I try to use some of them to analyse some data. More precisely, I try to use the function GOHyperg from package GOstats for Arabidopsis data. For the function GOhyperG, there is an example with the hgu95av2 package (human genome) and I would like to apply this example with the package ath1121501 (Arabidopsis package). But the function GOhyperG() uses a field called LOCUSID in the package hgu95av2. This field does not exist in the ath1121501 package...So, the function GOhyperG could not be applied to analyze arabidopsis data... So, could anyone indicate me how to find a solution? Thanks for your help. Olivier.
ath1121501 hgu95av2 gostats • 625 views
ADD COMMENTlink modified 13.1 years ago by Seth Falcon7.4k • written 13.1 years ago by Martin Olivier70
Answer: GOstats and library ath1121501
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gravatar for Seth Falcon
13.1 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Martin, > > Martin Olivier wrote: >> Hello, >> >> I don't know very well the bioconductor packages, but I try to use some >> of them to analyse >> some data. More precisely, I try to use the function GOHyperg from >> package GOstats for Arabidopsis data. > > One of the best resources we have is the mailing list, which can be > searched using gmane (link on BioC website under 'Join Mailing List'). > > This same question was asked about six days ago, and Nianhua Li was kind > enough to give a very detailed answer that can be found here: > > http://article.gmane.org/gmane.science.biology.informatics.conductor /9737/match=nianhua+gohyperg > > See her response under question #3. We are planning to make this easier, and hope to have something in the next release. For now, the workaround that Nianhua came up with should get you going. + seth
ADD COMMENTlink written 13.1 years ago by Seth Falcon7.4k
Answer: GOstats and library ath1121501
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gravatar for James W. MacDonald
13.1 years ago by
United States
James W. MacDonald51k wrote:
Hi Martin, Martin Olivier wrote: > Hello, > > I don't know very well the bioconductor packages, but I try to use some > of them to analyse > some data. More precisely, I try to use the function GOHyperg from > package GOstats for Arabidopsis data. One of the best resources we have is the mailing list, which can be searched using gmane (link on BioC website under 'Join Mailing List'). This same question was asked about six days ago, and Nianhua Li was kind enough to give a very detailed answer that can be found here: http://article.gmane.org/gmane.science.biology.informatics.conductor/9 737/match=nianhua+gohyperg See her response under question #3. HTH, Jim > > For the function GOhyperG, there is an example with the hgu95av2 package > (human genome) and I would like to apply > this example with the package ath1121501 (Arabidopsis package). But the > function GOhyperG() uses a field called LOCUSID > in the package hgu95av2. This field does not exist in the ath1121501 > package...So, the function GOhyperG could not be applied > to analyze arabidopsis data... > > So, could anyone indicate me how to find a solution? Thanks for your help. > > Olivier. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 13.1 years ago by James W. MacDonald51k
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