[BioC] Problem with decideTests - No p-val correction

[James W. MacDonald]

Hi Atul,

On 7/23/2013 2:48 PM, Atul Kakrana wrote:
> Hi Everybody,
>
> I am trying to analyze Affymetrix data using 'affy' and 'limma'
> packages. The problem I am facing is that results from decideTests()
> does not seem to have p-values corrected.
>
> Code snippet:
> ......
> AF.fit2<- eBayes(AF.fit2)
>
> ##Without p-value correction
> AF.results.global<- decideTests(AF.fit2, method =
> 'global',adjust.method = 'none')
> write.fit(AF.fit2,AF.results.global,file='AF_RESULTS_GLOB_wo_pval_adjust.tsv',
> sep = '\t')
>
> ##With p-val correction
> AF.results.global.Corr<- decideTests(AF.fit2, method =
> 'global',adjust.method = 'fdr',p.value= 0.05)
> write.fit(AF.fit2,AF.results.global.Corr,file='AF_RESULTS_GLOB.tsv', sep
> = '\t')
>
> ......
>
> Now when I check both the results, with and without p-val correction,
> they both have exactly same p-values. Which means that it does not makes
> any difference if I choose 'adjust.method' as 'none' or 'fdr'. Please
> tell me how can I correct p-values. I am sure I am missing something.

See the arguments for write.fit, in particular the 'adjust' argument.

Best,

Jim

>
> Thanks
>
> AK
>
>> sessionInfo()
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>    [1] virtualArray_1.2.1     preprocessCore_1.20.0  plyr_1.8               lumiMouseAll.db_1.18.0 org.Mm.eg.db_2.8.0     affycoretools_1.30.0
>    [7] KEGG.db_2.8.0          GO.db_2.8.0            RSQLite_0.11.4         DBI_0.2-7              genefilter_1.40.0      annotate_1.36.0
> [13] AnnotationDbi_1.20.7   sva_3.4.0              mgcv_1.7-23            corpcor_1.6.6          lumi_2.10.0            nleqslv_2.0
> [19] affy_1.36.1            limma_3.14.4           Biobase_2.18.0         BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>    [1] affyio_1.26.0         affyPLM_1.34.0        annaffy_1.30.0        AnnotationForge_1.0.3 BiocInstaller_1.8.3   biomaRt_2.14.0
>    [7] Biostrings_2.26.3     Category_2.24.0       colorspace_1.2-2      gcrma_2.30.0          gdata_2.12.0.2        GEOquery_2.24.1
> [13] GOstats_2.24.0        gplots_2.11.0         graph_1.36.2          grid_2.15.3           GSEABase_1.20.2       gtools_2.7.1
> [19] IRanges_1.16.6        KernSmooth_2.23-10    lattice_0.20-15       MASS_7.3-23           Matrix_1.0-12         methylumi_2.4.0
> [25] nlme_3.1-108          parallel_2.15.3       RBGL_1.34.0           RCurl_1.95-4.1        reshape2_1.2.2        splines_2.15.3
> [31] stats4_2.15.3         stringr_0.6.2         survival_2.37-4       tools_2.15.3          XML_3.96-1.1          xtable_1.7-1
> [37] zlibbioc_1.4.0
>
>
>
> 	[[alternative HTML version deleted]]
>
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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