[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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