[BioC] Rankprod- gene appearing in both up and down regulated lists?

Adam Cornwell [guest] guest at bioconductor.org
Wed Aug 21 19:18:27 CEST 2013

I am using RankProd for differential expression of array data. I've confirmed that all of my input gene names, rownames, etc are all gene-level and contain no duplicates. Yet, when I run RPadvance and look at the output of topGene(rankprodResult, cutoff=0.05, logged = TRUE, logbase=2)$Table1
topGene(rankprodResult, cutoff=0.05, logged = TRUE, logbase=2)$Table2
I see that there is one gene which appears in both of those lists- with the same fold change but different p-values for the occurrence in Table1 and Table2. I then went and confirmed that my initial input did not contain duplicates again- which is indeed the case. The foldchange is 1.2744, which seems to indicate that the gene is actually downregulated and should only be in Table2. 
rankprod.table1[rankprod.table1[,"FC:(class1/class2)"] >= 1,]
        gene.index            RP/Rsum FC:(class1/class2)                pfp            P.value 
        19582.0000          2031.3112             1.2744             0.0244             0.0017

What's going on here? I've used this method a few times before, and haven't seen this. I'm using the newest version of RankProd.

(While I'm asking this already- are all the p-values of 0 from underflowing or from the method used to calculate those values? It feels quite strange sometimes to be presenting all these p-values of 0 in my results.)

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[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] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pd.hugene.2.0.st_3.8.0                heatmap.plus_1.3                      RankProd_2.32.0                      
 [4] hugene20sttranscriptcluster.db_2.12.1 xlsx_0.5.1                            xlsxjars_0.5.0                       
 [7] rJava_0.9-4                           annotate_1.38.0                       org.Hs.eg.db_2.9.0                   
[10] GGally_0.4.4                          reshape_0.8.4                         plyr_1.8                             
[13] ggplot2_0.9.3.1                       biomaRt_2.16.0                        puma_3.2.1                           
[16] mclust_4.2                            VennDiagram_1.6.4                     scatterplot3d_0.3-33                 
[19] annaffy_1.32.0                        KEGG.db_2.9.1                         GO.db_2.9.0                          
[22] RSQLite_0.11.4                        DBI_0.2-7                             AnnotationDbi_1.22.6                 
[25] gplots_2.11.3                         KernSmooth_2.23-10                    caTools_1.14                         
[28] gdata_2.13.2                          gtools_3.0.0                          MASS_7.3-28                          
[31] RColorBrewer_1.0-5                    affyPLM_1.36.0                        preprocessCore_1.22.0                
[34] simpleaffy_2.36.1                     gcrma_2.32.0                          genefilter_1.42.0                    
[37] oligo_1.24.2                          oligoClasses_1.22.0                   affy_1.38.1                          
[40] marray_1.38.0                         limma_3.16.7                          Biobase_2.20.1                       
[43] BiocGenerics_0.6.0                   

loaded via a namespace (and not attached):
 [1] affxparser_1.32.3    affyio_1.28.0        BiocInstaller_1.10.3 Biostrings_2.28.0    bit_1.1-10           bitops_1.0-5        
 [7] codetools_0.2-8      colorspace_1.2-2     dichromat_2.0-0      digest_0.6.3         dynamicTreeCut_1.21  ff_2.2-11           
[13] foreach_1.4.1        GenomicRanges_1.12.4 gtable_0.1.2         impute_1.34.0        IRanges_1.18.3       iterators_1.0.6     
[19] labeling_0.2         munsell_0.4.2        proto_0.3-10         RCurl_1.95-4.1       reshape2_1.2.2       scales_0.2.3        
[25] splines_3.0.1        stats4_3.0.1         stringr_0.6.2        survival_2.37-4      tools_3.0.1          WGCNA_1.27-1        
[31] XML_3.98-1.1         xtable_1.7-1         zlibbioc_1.6.0      

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