Entering edit mode
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? ?
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