[BioC] PR, topGene and 'gene.names should have the same length as the gene vector'

[Martin Morgan]

Hi John --

On 05/13/2010 02:09 AM, John Coulthard wrote:
> 
> 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])

e[,0] returns a matrix of length 0

> library(Biobase)
> data(sample.ExpressionSet)
> length(exprs(sample.ExpressionSet)[,0])
[1] 0

whereas I think what you want is a character vector of length nrow(e)

> length(rownames(exprs(sample.ExpressionSet)))
[1] 500
> length(featureNames(sample.ExpressionSet))
[1] 500

Martin

> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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