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Question: pathview -- ID Problem?
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gravatar for Luo Weijun
5.1 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k 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 -------------------------------------------- Subject: Re: pathview -- ID Problem? 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 -------------------------------------------- wrote: 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 modified 5.1 years ago by fabian10 • written 5.1 years ago by Luo Weijun1.4k
0
gravatar for fabian
5.1 years ago by
fabian10
fabian10 wrote:
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 = > 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 written 5.1 years ago by fabian10
Fabian, Sorry for the confusion, I am glad that you figured it out. Weijun -------------------------------------------- On Fri, 11/1/13, fabian <fabian at="" tbi.univie.ac.at=""> wrote: Subject: Re: pathview -- ID Problem? Cc: bioconductor at r-project.org Date: Friday, November 1, 2013, 12:19 AM 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 > > -------------------------------------------- wrote: > >? Subject: Re: pathview -- ID Problem? >? To: bioconductor at r-project.org, fabian at tbi.univie.ac.at, >? 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 > >? -------------------------------------------- >? wrote: > >???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",? : >???? 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 REPLYlink written 5.1 years ago by Luo Weijun1.4k
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