
Dear list

I'm trying to do a rank porducts analysis on an expression set and I cannot get the gene names onto the results table.  The error is 'gene.names should have the same length as the gene vector' but I'm giving topGene column 0 of the data matrix I gave RP so how can they have different lengths?  What exactly is the 'gene vector' mentioned in the error?

My working below.
Many thanks for you time.

John

> class(lumidataB.bgt)
[1] "LumiBatch"
attr(,"package")
[1] "lumi"
> e <- exprs(lumidataB.bgt)
> head(e)
                                           17  18  19  20  21  22 23   24
Ku8QhfS0n_hIOABXuE   7.2 7.2 7.1 7.2 7.2 7.3 7.1 7.2
fqPEquJRRlSVSfL.8A      7.3 7.3 7.3 7.5 7.3 7.4 7.4 7.4
ckiehnugOno9d7vf1Q     7.3 7.2 7.2 7.3 7.3 7.2 7.3 7.3 
x57Vw5B5Fbt5JUnQkI    7.2 7.4 7.2 7.3 7.3 7.3 7.1 7.3 
ritxUH.kuHlYqjozpE       7.3 7.3 7.3 7.1 7.1 7.4 7.3 7.3 
QpE5UiUgmJOJEkPXpc  7.2 7.2 7.2 7.2 7.4 7.2 7.2 7.2

> design <- c(0,0,0,0,1,1,1,1)
> rp.out<-RP(e,design,logged=TRUE,plot=TRUE, num.perm = 100)
Rank Product analysis for two-class case 
 
Starting 100 permutations... 
Computing pfp .. 
Outputing the results .. 
> topGene(rp.out, cutoff=0.005, method="pfp",gene.names=e[,0])
Warning: gene.names should have the same length as the gene vector. 
No gene.names are assigned 




> sessionInfo()
R version 2.10.1 (2009-12-14) 
i386-redhat-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

other attached packages:
 [1] RankProd_2.18.0          lumiHumanAll.db_1.8.1   
 [3] org.Hs.eg.db_2.3.6       beadarray_1.14.0        
 [5] lumiHumanIDMapping_1.4.0 lumi_1.12.4             
 [7] MASS_7.3-4               RSQLite_0.8-4           
 [9] DBI_0.2-5                preprocessCore_1.8.0    
[11] mgcv_1.6-1               annotate_1.24.1         
[13] AnnotationDbi_1.8.2      affy_1.24.2             
[15] Biobase_2.6.1            limma_3.2.3             

loaded via a namespace (and not attached):
[1] affyio_1.14.0      grid_2.10.1        hwriter_1.2       
[4] KernSmooth_2.23-3  lattice_0.17-26    Matrix_0.999375-33
[7] nlme_3.1-96        tools_2.10.1       xtable_1.5-6      



 		 	   		  
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