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Last seen 10.5 years ago
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
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