[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.

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[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       

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