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

Linda [guest] guest at bioconductor.org
Mon Dec 16 15:43:19 CET 2013


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)
[1] "list"
[1] "data.frame"
#as the "mode" is "list" I unlisted:
FDRunlist <- unlist(FDR)

[1] TRUE
[1] "numeric"
[1] "numeric"
[1] "19" "20" "52" "59" "87"
        19         20         52         59        87
-0.6840078  0.3224513 -0.4224444 -0.1587436  0.7630991 

 100652853  100861532  100874195  100996255  100996511   
 0.7640486  1.0621681 -0.4461532  0.7015199  0.5199217  

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)

[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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