Question: topTable gene list
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gravatar for daphne mouzaki RI
13.2 years ago by
daphne mouzaki RI80 wrote:
hi, I have generated a list of significant genes for 3 time points separately using the function "decideTests"in Limma package.Using this function I generated foldchanges and FDR for every gene using method Benjamini and Hochberg ("BH") and p.value=0.05. I was wondering if it is possible to generate all the FDR and foldchanges with the respective gene name for every time point. I tried changing the cut-off to 1 in order not to exclude anything and the method set to the function "decideTests" changed to "none" but it doesn't work. Could you recommend any other possible ways? I would appreciate any help, Daphne
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ADD COMMENTlink modified 13.2 years ago by Giovanni Coppola250 • written 13.2 years ago by daphne mouzaki RI80
Answer: topTable gene list
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gravatar for Giovanni Coppola
13.2 years ago by
Giovanni Coppola250 wrote:
Hi Daphne, perhaps ?write.fit does what you want. Best Giovanni On Sep 13, 2006, at 7:13 AM, daphne mouzaki ((RI)) wrote: > hi, > > I have generated a list of significant genes for 3 time points > separately using the function > "decideTests"in Limma package.Using this function I generated > foldchanges and FDR for every > gene using method Benjamini and Hochberg ("BH") and p.value=0.05. > I was wondering if it is possible to generate all the FDR and > foldchanges with the respective > gene name for every time point. > I tried changing the cut-off to 1 in order not to exclude anything and > the method set to the > function "decideTests" changed to "none" but it doesn't work. > Could you recommend any other possible ways? > > I would appreciate any help, > > Daphne > > _______________________________________________ > 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
ADD COMMENTlink written 13.2 years ago by Giovanni Coppola250
Answer: topTable gene list
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gravatar for James W. MacDonald
13.2 years ago by
United States
James W. MacDonald51k wrote:
daphne mouzaki (RI) wrote: > hi, > > I have generated a list of significant genes for 3 time points > separately using the function > "decideTests"in Limma package.Using this function I generated > foldchanges and FDR for every > gene using method Benjamini and Hochberg ("BH") and p.value=0.05. > I was wondering if it is possible to generate all the FDR and > foldchanges with the respective > gene name for every time point. If you want everything then decideTests() is probably not the function you want. Instead, you should try topTable(). Something like this should work: topTable(<marraylm object="">, coef = 1, number = <number of="" genes="" on="" chip="">) You can then change 'coef' to 2, 3,... depending on the number of contrasts you have. HTH, Jim > I tried changing the cut-off to 1 in order not to exclude anything and > the method set to the > function "decideTests" changed to "none" but it doesn't work. > Could you recommend any other possible ways? > > I would appreciate any help, > > Daphne > > _______________________________________________ > 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 13.2 years ago by James W. MacDonald51k
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