[BioC] PGSEA and smcPlot

Iain Gallagher iaingallagher at btopenworld.com
Wed Jul 27 20:44:55 CEST 2011

Hi List

I'm using PGSEA  and I would like to plot the results of my analysis using the smcPlot function in the package.

Using this function appends a row labelled 'GS' at the bottom of the plot. I would like to use custom row labels for my plot and have created a vector of names as suggested in the package documentation. 

When I try to use this I get the following error:

Error in axis(4, 1:nrow(m), las = 2, line = -0.5, tick = 0, labels = rnames,  : 
  'at' and 'labels' lengths differ, 52 != 51

suggesting that my rnames vector and the number of rows in the matrix used for the plot have different lengths. They don't however - both are 51.

The 'GS' not in the matrix before it goes into the plotting function (smcPlot) and I can't see anything indicating that this is added in the plotting function.

I've also tried adding a 'dummy' label to my vector of row labels (i.e. to make it 52 in length) but the result is the same.

Could anyone enlighten me?



> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           

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

other attached packages:
 [1] pheatmap_0.3         limma_3.6.6          PGSEA_1.14.0        
 [4] samr_1.28            impute_1.26.0        GOstats_2.18.0      
 [7] graph_1.30.0         Category_2.16.0      genefilter_1.32.0   
[10] hgu133plus2.db_2.4.5 org.Hs.eg.db_2.4.6   RSQLite_0.9-4       
[13] DBI_0.2-5            annotate_1.28.0      AnnotationDbi_1.14.1
[16] affy_1.28.0          Biobase_2.10.0      

loaded via a namespace (and not attached):
 [1] affyio_1.18.0         colorspace_1.0-1      GO.db_2.5.0          
 [4] grid_2.13.1           GSEABase_1.12.1       preprocessCore_1.12.0
 [7] RBGL_1.28.0           splines_2.13.1        survival_2.36-9      
[10] tools_2.13.1          XML_3.4-0             xtable_1.5-6         

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