[BioC] operations are possible only for numeric, logical or complex types

[Luo Weijun]

Hi Linda,
Sorry I didn’t notice your question on pathview because of the subject line didn’t seem to be related.
Several pathview arguments have to be a list of two elements with "gene" and "cpd" as the names, even though "cpd" value has no actual effect for your case. These include limit, discrete, bins, both.dirs, trans.fun, low, mid, and high. Please check the help info for details:
?pathview

So you last call should be:
pv.out  <- pathview(gene.data=FDRunlist,
 pathway.id="04930", gene.idtype = "entrez", species="hsa",
 out.suffix="FDR", limit=list(gene=3.5, cpd=1),
 discrete=list(gene=F, cpd=F))

you may actually drop discrete argument in a whole above as that’s the default.
HTH,
Weijun

--------------------------------------------


 Subject: operations are possible only for numeric, logical or complex types
 To: bioconductor at r-project.org, lindazuurbier at yahoo.ca

 Date: Monday, December 16, 2013, 9:43 AM


 Hi, 

 I try to use pathview using a list of fold-changes obtained
 from microarray data, with corresponding ENTREZ ID's.
 Running the last command I encouter the error:

 Error in discrete & disc.cond1 : 
   operations are possible only for numeric, logical or
 complex types

 I don't understand what the problem is as, to my opinion, my
 data input is numeric. 

 I did it as follows:

 #this table is just a txt file with two columns; one #with
 ENTREZ ID's and one with fold-changes.
 FDR <- read.table("Foldchange.txt", dec=",", header=T,
 check.names=FALSE)
 mode(FDR)
 [1] "list"
 class(FDR)
 [1] "data.frame"
 #as the "mode" is "list" I unlisted:
 FDRunlist <- unlist(FDR)

 is.vector(FDRunlist)
 [1] TRUE
 class(FDRunlist)
 [1] "numeric"
 mode(FDRunlist)
 [1] "numeric"
 names(FDRunlist)[1:5]
 [1] "19" "20" "52" "59" "87"
 head(FDRunlist)
         19     
    20     
    52     
    59        87
 -0.6840078  0.3224513 -0.4224444 -0.1587436 
 0.7630991 
        102
 -0.4196958

 tail(FDRunlist)
  100652853  100861532  100874195 
 100996255  100996511   
  0.7640486  1.0621681 -0.4461532  0.7015199 
 0.5199217  
 100996870
 0.4943131 

 This data looks exactly the same as the gse16873.t example
 file (except for the negative values) so I don't know why I
 got the error after the next line: 

 pv.out  <- pathview(gene.data=FDRunlist,
 pathway.id="04930", gene.idtype = "entrez", species="hsa",
 out.suffix="FDR",  limit=list(gene=3.5),
 discrete=list(gene=F))

 I hope somebody can help me out! 







  -- output of sessionInfo(): 

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

 locale:
 [1] LC_COLLATE=Dutch_Netherlands.1252 
 LC_CTYPE=Dutch_Netherlands.1252   
 LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C   
                
    LC_TIME=Dutch_Netherlands.1252 
   

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

 other attached packages:
  [1] pathview_1.1.4   
    KEGGgraph_1.16.0 
    graph_1.38.3     
    XML_3.98-1.1     
    affyio_1.28.0       
 survival_2.37-4      multtest_2.16.0 
     annotate_1.38.0     
 hgu133plus2.db_2.9.0
 [10]
 org.Hs.eg.db_2.9.0   RSQLite_0.11.4 
      DBI_0.2-7     
       AnnotationDbi_1.22.6 vsn_3.28.0 
          affy_1.38.1 
         Biobase_2.20.1   
    BiocGenerics_0.6.0  

 loaded via a namespace (and not attached):
  [1] BiocInstaller_1.10.4  grid_3.0.1   
         IRanges_1.18.4   
     lattice_0.20-24   
    limma_3.16.8       
   MASS_7.3-29       
    png_0.1-7       
      preprocessCore_1.22.0
  [9] Rgraphviz_2.4.1   
    stats4_3.0.1       
   xtable_1.7-1         
 zlibbioc_1.6.0  

 --
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