User: Goeman, J.J. MSTAT

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Posts by Goeman, J.J. MSTAT

<prev • 15 results • page 1 of 2 • next >
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globaltest 5.6.1 bug fix
... A bug was found and fixed in globaltest that made the test sometimes ignore covariates under the null hypothesis if a Cox model was used. If you are using globaltest with survival data, please update to version 5.6.1 (release) or 5.7.4 (devel). Jelle www.lumc.nl/goeman ...
survival globaltest written 8.3 years ago by Goeman, J.J. MSTAT150
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globaltest 5.0.2
... A big was fixed in the release version of globaltest that gave an error message in survival models with covariates. Please update to globaltest 5.0.2 if you are using survival data. Jelle ...
survival globaltest written 9.8 years ago by Goeman, J.J. MSTAT150
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bug fix in globaltest
... Dear all, A bug was fixed in globaltest that sometimes resulted in wrong gene labels in the features() plot. Please update your package installation to version 5.0.1 (release) or 5.1.2 (devel). Apologies for any incovenience. Jelle ...
globaltest written 9.9 years ago by Goeman, J.J. MSTAT150
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Positions at the Department of Medical Statistics and Bioinformatics in Leiden
... Two positions are available at the Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, The Netherlands. We are looking for an * Assistant Professor (Biostatistician) Specializing in statistical methods for modern high throughput biology (-omics), and a ...
written 11.4 years ago by Goeman, J.J. MSTAT150
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Comment: C: Cox Model
... Dear Eleni, If you are interested in prediction of survival with (a subset of) your 18000 genes, you may want to have a look at the "penalized" package on CRAN (http://cran.us.r-project.org/src/contrib/Descriptions/penalized.html) or other packages there that do penalized estimation. Jelle > ...
written 11.7 years ago by Goeman, J.J. MSTAT150
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Answer: A: globaltest - multinomial model
... 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 ...
written 12.2 years ago by Goeman, J.J. MSTAT150
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Answer: A: globaltest Error when using subset data
... Dear Xia, This is a recently discovered bug that occurs in the permutation version of the test when there are empty genesets (which have empty intersection with the set of gene names). As globaltest automatically selects the permutation version of the test when there are few samples, the bug only ...
written 12.7 years ago by Goeman, J.J. MSTAT150
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globaltest: pairwise design?
... Hi Mette, > We have one-color ABI-data from 3 persons at 2 timepoints (a pilot > study), and want to compare the gene expression at the two timepoints > for a group of genes. > We could forget that the same person gave rise to two correlated values > in time and run globaltest with ...
globaltest written 13.1 years ago by Goeman, J.J. MSTAT150
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Comment: C: Error message: no package 'file5f906952' was found
... Dear Wonjong, I've had a very similar error e few months ago. It can occur after a failed installation of some other package, which was not removed from its temporary folder. Probably there is a folder called file5f906952 in your R/library folder. Try removing that folder and doing the installati ...
written 13.1 years ago by Goeman, J.J. MSTAT150
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Comment: C: globaltest question
... Dear Mike, The permutation version of globaltest is safe but conservative for small sample size. It can always be used, even in small groups, but it is not so useful if you want to test many pathways because a Bonferroni or FDR correction may leave you with no significant pathways at all due to th ...
written 13.1 years ago by Goeman, J.J. MSTAT150

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