Dear Users, I am using Limma package to identify the DEGs, toptable() was used to define the adjusted p-value, now as project requested, it has to be selected by p-value, instead of adjusted p-value. Does anyone know what function should I use? Any input would be appreciated. Thanks -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] VennDiagram_1.6.4 pd.hugene.2.0.st_3.8.0 oligo_1.24.1 [4] oligoClasses_1.22.0 hugene20sttranscriptcluster.db_2.12.1 org.Hs.eg.db_2.9.0 [7] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 [10] limma_3.16.6 affy_1.38.1 Biobase_2.20.1 [13] BiocGenerics_0.6.0 BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 ff_2.2-11 [7] foreach_1.4.1 GenomicRanges_1.12.4 IRanges_1.18.2 iterators_1.0.6 preprocessCore_1.22.0 splines_3.0.1 [13] stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

On 8/5/2013 11:27 AM, guest [guest] wrote: > Dear Users, > > I am using Limma package to identify the DEGs, toptable() was used to define the adjusted p-value, now as project requested, it has to be selected by p-value, instead of adjusted p-value. Does anyone know what function should I use? The topTable output lists both adjusted and unadjusted p-values. In addition, there is an argument to topTable() that allows you to specify the p-value adjustment. Best, Jim > > Any input would be appreciated. > Thanks > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] VennDiagram_1.6.4 pd.hugene.2.0.st_3.8.0 oligo_1.24.1 > [4] oligoClasses_1.22.0 hugene20sttranscriptcluster.db_2.12.1 org.Hs.eg.db_2.9.0 > [7] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 > [10] limma_3.16.6 affy_1.38.1 Biobase_2.20.1 > [13] BiocGenerics_0.6.0 BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] affxparser_1.32.3 affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 ff_2.2-11 > [7] foreach_1.4.1 GenomicRanges_1.12.4 IRanges_1.18.2 iterators_1.0.6 preprocessCore_1.22.0 splines_3.0.1 > [13] stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099