Question: KEGGSOAP incomplete list.pathways
0
gravatar for Guest User
7.9 years ago by
Guest User12k
Guest User12k wrote:
hi, I'm finding a discrepancy with KEGGSOAP for arabidopsis. Not all the pathways are returned via list.pathways. I'm trying to get the text definition of identified pathways for example: get.pathways.by.genes('ath:AT5G14780') [1] "path:ath00630" "path:ath01100" yet 00630 is not within the 63 pathways: [1] "path:ath00603" [1] "path:ath00620" [1] "path:ath00640" [1] "path:ath00660" [1] "path:ath00710" I do get a warning: Warning message: In matrix(unlist(.SOAP(KEGGserver, "list_pathways", .soapArgs = list(org = org), : data length [125] is not a sub-multiple or multiple of the number of rows [63] thanks for the help, and let me know if you need more information, kevin -- output of sessionInfo(): R version 2.14.0 (2011-10-31) Platform: x86_64-pc-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] stats graphics grDevices utils datasets methods base other attached packages: [1] SSOAP_0.8-0 org.At.tair.db_2.6.4 RSQLite_0.10.0 [4] DBI_0.2-5 AnnotationDbi_1.16.2 Biobase_2.14.0 [7] KEGGSOAP_1.28.0 loaded via a namespace (and not attached): [1] IRanges_1.12.1 RCurl_1.7-0 XML_3.4-3 XMLSchema_0.1-6 -- Sent via the guest posting facility at bioconductor.org.
pathways keggsoap • 538 views
ADD COMMENTlink modified 7.9 years ago by Marc Carlson7.2k • written 7.9 years ago by Guest User12k
Answer: KEGGSOAP incomplete list.pathways
0
gravatar for Marc Carlson
7.9 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Kevin, Thank you for reporting this. But I fear you are probbaly reporting this to the wrong group. The KEGGSOAP package is unlike most other bioconductor annotation packages in that it is actually a thin wrapper around KEGGs SOAP API. The discrepancy you are seeing is generated by their two SOAP methods. I actually have no idea why list.pathways (which is really the list_pathways method from their API), does not return "path:ath00630", but I bet that they would like to know this is happening. This is the site that describes their API: http://www.genome.jp/kegg/docs/keggapi_manual.html#label:36 And this is probably who you should contact: http://www.genome.jp/kegg/anniversary/contact.html Now that warning that you saw was coming from the XML package, (which KEGGSOAP depends on to learn about the existence of all these methods). The warning means that XML might be causing us some other trouble too (which we are investigating), but it is probably not going to cause the kind of trouble you described here. Marc On 11/18/2011 01:34 PM, kevin [guest] wrote: > hi, > > I'm finding a discrepancy with KEGGSOAP for arabidopsis. Not all the pathways are returned via list.pathways. I'm trying to get the text definition of identified pathways > > for example: > get.pathways.by.genes('ath:AT5G14780') > [1] "path:ath00630" "path:ath01100" > > yet 00630 is not within the 63 pathways: > [1] "path:ath00603" > [1] "path:ath00620" > > [1] "path:ath00640" > [1] "path:ath00660" > [1] "path:ath00710" > > I do get a warning: > Warning message: > In matrix(unlist(.SOAP(KEGGserver, "list_pathways", .soapArgs = list(org = org), : > data length [125] is not a sub-multiple or multiple of the number of rows [63] > > thanks for the help, and let me know if you need more information, > kevin > > > -- output of sessionInfo(): > > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] SSOAP_0.8-0 org.At.tair.db_2.6.4 RSQLite_0.10.0 > [4] DBI_0.2-5 AnnotationDbi_1.16.2 Biobase_2.14.0 > [7] KEGGSOAP_1.28.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.12.1 RCurl_1.7-0 XML_3.4-3 XMLSchema_0.1-6 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.9 years ago by Marc Carlson7.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 230 users visited in the last hour