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

[Atul Kakrana]

Hi James,

Thanks for the tip.

AK


On 23-Jul-13 3:09 PM, James W. MacDonald wrote:
> 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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>