globaltest - multinomial model
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@hans-ulrich-klein-1945
Last seen 3 days ago
United States
Hi List, I get a warning message whenever I use the function globaltest with a multinomial model. Below is a code example taken from the vignette leading to the warning message: Warning message: $ operator not defined for this S4 class, returning NULL in: fit$iter Should I be concerned about the warning message? Regards, Hans-Ulrich > library(globaltest) > library(golubEsets) > library(vsn) > data(Golub_Merge) > Golub <- Golub_Merge[, 1:34] > exprs(Golub) <- exprs(vsn2(Golub_Merge[, 1:34])) > globaltest(Golub, "Source") Global Test result: Data: 34 samples with 7129 genes; 1 gene set Model: multinomial Method: Asymptotic distribution Genes Tested Statistic Q Expected Q sd of Q P-value all 7129 7129 23.126 10 1.9632 2.5091e-05 Warning message: $ operator not defined for this S4 class, returning NULL in: fit$iter > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale: C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: vsn limma affy affyio golubEsets globaltest multtest "2.2.0" "2.10.0" "1.14.2" "1.4.1" "1.4.3" "4.6.0" "1.16.1" survival Biobase "2.32" "1.14.1"
Survival affy vsn limma globaltest affyio Survival affy vsn limma globaltest affyio • 719 views
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@goeman-jj-mstat-696
Last seen 7.1 years ago
Dear Hans-Ulrich, This is a minor bug, which has, I believe, been fixed in the latest devel version. The worst thing that can happen is that you miss a warning that the null model did not converge before the maximum number of iterations. If you want you can check this by asking for fit(gt)@iter after gt <- globaltest(Golub, "Source") If this is smaller than 20 the null model has converged. Regards, Jelle > -----Original Message----- > From: Hans-Ulrich Klein [mailto:h.klein at uni-muenster.de] > Sent: 16 August 2007 19:31 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] globaltest - multinomial model > > Hi List, > > I get a warning message whenever I use the function globaltest with a > multinomial model. Below is a code example taken from the vignette > leading to the warning message: > Warning message: > $ operator not defined for this S4 class, returning NULL in: fit$iter > > Should I be concerned about the warning message? > > Regards, > Hans-Ulrich > > > > > library(globaltest) > > library(golubEsets) > > library(vsn) > > data(Golub_Merge) > > Golub <- Golub_Merge[, 1:34] > > exprs(Golub) <- exprs(vsn2(Golub_Merge[, 1:34])) > > > globaltest(Golub, "Source") > Global Test result: > Data: 34 samples with 7129 genes; 1 gene set > Model: multinomial > Method: Asymptotic distribution > > Genes Tested Statistic Q Expected Q sd of Q P-value > all 7129 7129 23.126 10 1.9632 2.5091e-05 > Warning message: > $ operator not defined for this S4 class, returning NULL in: fit$iter > > > > sessionInfo() > R version 2.5.0 (2007-04-23) > x86_64-unknown-linux-gnu > > locale: > C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" > "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > vsn limma affy affyio golubEsets globaltest > multtest > "2.2.0" "2.10.0" "1.14.2" "1.4.1" "1.4.3" "4.6.0" > "1.16.1" > survival Biobase > "2.32" "1.14.1" > > >
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