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Question: pathview -- ID Problem?
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4.8 years ago by
Guest User12k
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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 = evalas.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.
ADD COMMENTlink modified 4.8 years ago by Luo Weijun1.4k • written 4.8 years ago by Guest User12k
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4.8 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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 -------------------------------------------- Subject: pathview -- ID Problem? To: bioconductor at r-project.org, fabian at tbi.univie.ac.at 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 = evalas.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",? : [[elided Yahoo spam]] 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.
ADD COMMENTlink written 4.8 years ago by Luo Weijun1.4k
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