[BioC] Limma: how to set the selection by p-value
guest [guest]
guest at bioconductor.org
Mon Aug 5 17:27:59 CEST 2013
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.
More information about the Bioconductor
mailing list