Parsing ./spoNA.xml file failed, please check the file!

Question

[Parham]

I am trying the pathway analysis from this workflow (1). I recieve error that parsing some file failed! Other question I have is, if it is enough to just change the species="hsa" to species="spo" for s. pombe or I need to change the codes upstream also? (1) RNA-Seq Data Pathway and Gene-set Analysis Workflows - Weijun Luo.

> gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union", ignore.strand=TRUE, param=param)
> dim(gnCnt)
[1] 7017    2
> pfh1.cnts=assay(gnCnt)
> cnts=pfh1.cnts
> dim(cnts)
[1] 7017    2
> sel.rn=rowSums(cnts) !=0
> cnts=cnts[sel.rn,]
> dim(cnts)
[1] 5968    2
> library(DESeq2)
Loading required package: Rcpp
Loading required package: RcppArmadillo
> grp.idx <- rep(c("cotnrol", "experiment")
+ 
> grp.idx <- rep(c("cotnrol", "experiment"))
> coldat=DataFrame(grp=factor(grp.idx))
> dds <- DESeqDataSetFromMatrix(cnts, colData=coldat, design= ~ grp)
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
same number of samples and coefficients to fit, estimating dispersion by treating samples as replicates
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> deseq2.res <- results(dds)
> deseq2.fc=deseq2.res$log2FoldChange
> names(deseq2.fc)=rownames(deseq2.res)
> exp.fc=deseq2.fc
> out.suffix="deseq2"
> require(gage)
Loading required package: gage
> kg.spo=kegg.gsets("spo")
> fc.kegg.p <- gage(exp.fc, gsets=kg.spo, ref=NULL, samp=NULL)
> sel <- fc.kegg.p$greater[, "q.val"] < 0.1 & !is.na(fc.kegg.p$greater[, "q.val"])
> path.ids <- rownames(fc.kegg.p$greater)[sel]
> sel.l <- fc.kegg.p$less[, "q.val"] < 0.1 & !is.na(fc.kegg.p$less[,"q.val"])
> path.ids.1 <- rownames(fc.kegg.p$less)[sel.l]
> path.ids2 <- substr(c(path.ids, path.ids.l), 1, 8)
Error in substr(c(path.ids, path.ids.l), 1, 8) : 
  error in evaluating the argument 'x' in selecting a method for function 'substr': Error: object 'path.ids.l' not found
> path.ids2 <- substr(c(path.ids, path.ids.1), 1, 8)
> require(pathview)
Loading required package: pathview
Loading required package: KEGGgraph
Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

The following object is masked from 'package:Biostrings':

    complement

Loading required package: org.Hs.eg.db
Loading required package: DBI

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html.

The pathview downloads and uses KEGG data. Academic users may freely use the
KEGG website at http://www.kegg.jp/ or its mirror site at GenomeNet
http://www.genome.jp/kegg/. Academic users may also freely link to the KEGG
website. Non-academic users may use the KEGG website as end users for
non-commercial purposes, but any other use requires a license agreement
(details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
> pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(gene.data= exp.fc, pathway.id = pid, species= "spo", out.suffix=out.suffix))
Getting gene ID data from KEGG...
Done with data retrieval!
[1] "Downloading xml files for spoNA, 1/1 pathways.."
[1] "Downloading png files for spoNA, 1/1 pathways.."
Download of spoNA xml and png files failed!
Failed to download KEGG xml/png files, spoNA skipped!
Getting gene ID data from KEGG...
Done with data retrieval!
Start tag expected, '<' not found
Parsing ./spoNA.xml file failed, please check the file!
Getting gene ID data from KEGG...
Done with data retrieval!
Start tag expected, '<' not found
Parsing ./spoNA.xml file failed, please check the file!
Warning message:
In download.file(png.url, png.target, quiet = T, mode = "wb") :
  cannot open: HTTP status was '404 Not Found'

[Pierre Lindenbaum]

cross posted: http://seqanswers.com/forums/showpost.php?p=143019&postcount=1

[Ram]

Is this a bad thing, Pierre?

[Pierre Lindenbaum]

not at all as you've waited for a long time to get an anwser :-) But people might have a look at SeqAnswers before answering here.

[Ram]

I beg to differ. I think BioStars is more responsive (not to mention that it has a better UX too) than SeqAnswers. But yes, this linking will ensure that answers are not duplicated (assuming we don't go ahead anyway for the virtual internet points involved :) )

Tl;DR: Thank you

[Ram]

Hi,

Please add the source link to the workflow. Also, please paste the first 25 lines of ./spoNA.xml (the output of head -n 25 spoNA.xml so we have some context on the contents of the XML file.

Thank you.

[Parham]

Hi, I updated the whole workflow and what I had done from a very earlier point! For ./spoNA.xml I get this error:

> head -n 25 spoNA.xml
Error: unexpected numeric constant in "head -n 25"

[Ram]

I'm sorry, head is a Unix command. Because the actual content of the file would help in checking for parse errors, could you maybe run the command from the Unix Command prompt or Mac terminal and paste the output here? Thank you!