[BioC] pathview -- ID Problem?

fabian fabian at tbi.univie.ac.at
Fri Nov 1 05:19:22 CET 2013


Hello

It took me a while but I figured that. Anyway, thank you very much for 
coming back to me for this correction.

Best
Fabian

On 01-11-2013 01:03, Luo Weijun wrote:
> There was a typo in my original response, id.type should be
> gene.idtype. The correct one is:
> ..., for you data, you need to specify gene.idtype="kegg" with 
> pathview.
> pv.out <- pathview(gene.data = data_bac_values, pathway.id = "05132",
> species = "sey", gene.idtype ="kegg", out.suffix = "test", kegg.native
> = T, same.layer = F)
> Weijun
> 
> --------------------------------------------
> On Fri, 10/18/13, Luo Weijun <luo_weijun at yahoo.com> wrote:
> 
>  Subject: Re: pathview -- ID Problem?
>  To: bioconductor at r-project.org, fabian at tbi.univie.ac.at, 
> fabian at yahoo.com
>  Date: Friday, October 18, 2013, 2:53 PM
> 
>  Dear Fabian,
>  You need to update your pathview to the latest release
>  version, which is 1.2.0. It is at:
>  http://bioconductor.org/packages/release/bioc/html/pathview.html
>  This current release version includes all recent update
>  features, like multiple samples/time series in one graph,
>  and handling of all KEGG species.Your version is
>  pathview_1.1.4, which doesn’t really handle many minor
>  KEGG species. To ensure smooth installation, I would suggest
>  you update your R/Bioconductor to the latest version too. Of
>  course, you may always download and install pathview_1.2.0
>  manually from the link above.
> 
>  BTW, for you data, you need to specify id.type="kegg" with
>  pathview.
>  pv.out <- pathview(gene.data = data_bac_values,
>  pathway.id = "05132", species = "sey", id.type="kegg",
>  out.suffix = "test", kegg.native = T, same.layer = F)
>  Read subsection 7.5 Working with species in the new vignette
>  for more details.
>  Weijun
> 
>  --------------------------------------------
>  On Fri, 10/18/13, fabian at yahoo.com
>  <fabian at yahoo.com>
>  wrote:
> 
>   Subject: pathview -- ID Problem?
>   To: bioconductor at r-project.org,
>  fabian at tbi.univie.ac.at
>   Cc: "pathview Maintainer" <luo_weijun at yahoo.com>
>   Date: Friday, October 18, 2013, 1:46 PM
> 
> 
>   Hello Mr. Weijun Luo
> 
>   I started to use pathview to visualize my differential
>  gene
>   expressin analysis. It is really a great help. First I
>   worked with human data and had no problem at all to make
>  it
>   run.
> 
>   Meanwhile I apply bacterial data and do not succeed. I'm
>  not
>   sure why. Here is my problem
> 
>   When I run the analysis with my input
> 
>   head(data_bac_values)
>   SL1344_0001 SL1344_0002 SL1344_0003 SL1344_0004
>  SL1344_0005
>   SL1344_0006
>     0.1329739   0.4947647 
>   -1.4013626   0.5086116  -4.0000000 
>   -0.2028169
> 
>   with the following command:
> 
>   > pv.out <- pathview(gene.data = data_bac_values,
>   pathway.id = "05132", species = "sey", out.suffix =
>  "test",
>   kegg.native = T, same.layer = F)
>   Error in mol.data[as.character(items[hit]), ] : subscript
>   out of bounds
>   In addition: Warning messages:
>   1: In node.map(gene.data, node.data, node.types =
>   gene.node.type, node.sum = node.sum) :
>     NAs introduced by coercion
>   2: In FUN(1:27[[1L]], ...) : NAs introduced by coercion
> 
>   This is the error thrown out. traceback() informs like
>   this:
> 
>   > traceback()
>   7: cbind(mol.data[as.character(items[hit]), ])
>   6: apply(cbind(mol.data[as.character(items[hit]), ]), 2,
>   node.sum,
>          na.rm = T)
>   5: FUN(1:27[[1L]], ...)
>   4: lapply(X = X, FUN = FUN, ...)
>   3: sapply(1:n.nodes, function(i) {
>          kns =
>   node.data$kegg.names[[i]]
>          if (node.types[1] == "gene")
> 
>              items =
>   as.numeric(kns)
>          else items = kns
>          ord = order(items)
>          items = items[ord]
>          kns = kns[ord]
>          hit = items %in% genes
>          if (sum(hit) == 0) {
>          
>      return(c(kns[1], spacials[i, ], rep(NA,
>   ncol(mol.data))))
>          }
>          else if (sum(hit) == 1) {
>              edata =
>   mol.data[as.character(items[hit]), ]
>          
>      return(c(kns[hit], spacials[i, ], edata))
>          }
>          else {
>              node.sum =
>   eval(as.name(node.sum))
>              edata =
>   apply(cbind(mol.data[as.character(items[hit]),
>              
>      ]), 2, node.sum, na.rm = T)
>          
>      return(c(kns[hit][1], spacials[i, ],
>   edata))
>          }
>      })
>   2: node.map(gene.data, node.data, node.types =
>   gene.node.type, node.sum = node.sum)
>   1: pathview(gene.data = data_bac_values, pathway.id =
>   "05132", species = "sey",
>          out.suffix = "test",
>   kegg.native = T, same.layer = F)
> 
> 
>   I'm aware from the mailing list that KEGG is not very
>   consistant with their ID scheme, which causes trouble. I
>   rechecked, the Id I use (Refseq locus tag) is also used by
>   KEGG (e.g. http://www.genome.jp/dbget-bin/www_bget?sey:SL1344_0001
>   works fine); I tried it with other IDs which I specified
>  via
>   gene.idtype and get the error:
> 
>   > pv.out <- pathview(gene.data = data_bac_values,
>   gene.idtype = "UNIPROT", pathway.id = "05132" ,species =
>   "sey", out.suffix = "test", kegg.native = T, same.layer =
>   F)
>   Error in pathview(gene.data = data_bac_values, gene.idtype
>  =
>   "UNIPROT",  :
>     No proper gene annotation package available!
> 
>   This is also truefor other IDs (of course I change each
>  time
>   the input file accordingly).
> 
>   Do you have any idea what causes the problem? any hint
>  would
>   be very much appreciated. Thank you very much in advance.
> 
>   best
>   Fabian
> 
>    -- output of sessionInfo():
> 
>   > sessionInfo()
>   R version 3.0.1 (2013-05-16)
>   Platform: x86_64-redhat-linux-gnu (64-bit)
> 
>   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=en_US.UTF-8   
>   LC_MESSAGES=en_US.UTF-8   
>    [7] LC_PAPER=C           
>        LC_NAME=C     
>              
>    [9] LC_ADDRESS=C           
>      LC_TELEPHONE=C       
>      
>   [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 
>        
> 
>   attached base packages:
>   [1] parallel  stats 
>      graphics  grDevices utils 
>      datasets  methods 
>   [8] base     
> 
>   other attached packages:
>    [1] pathview_1.1.4   
>      org.Hs.eg.db_2.9.0   RSQLite_0.11.4 
>      
>    [4] DBI_0.2-7           
>   AnnotationDbi_1.22.6 Biobase_2.20.1     
>    [7]
>   BiocGenerics_0.6.0   KEGGgraph_1.16.0 
>      graph_1.38.3       
>   [10] XML_3.98-1.1       
> 
>   loaded via a namespace (and not attached):
>   [1] grid_3.0.1      IRanges_1.18.4 
>   png_0.1-6       Rgraphviz_2.4.1
>   [5] stats4_3.0.1    tools_3.0.1   
> 
> 
>   --
>   Sent via the guest posting facility at bioconductor.org.



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