[BioC] Limma: how to set the selection by p-value

[James W. MacDonald]

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
>
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099