Hi, I am a beginner trying to do RNA Seq in R and currently facing issues while trying to do KEGG Pathway analysis. After running the tmp command, it appears that the pathway doesn't exsist. Out of the 5, I have got I pathway and not the rest. It would really great if you can help me out.
keggresids
[1] "hsa04614" "hsa04142" "hsa04145" "hsa04141" "hsa00980"
tmp=sapply(keggresids,function(pid)pathview(gene.data=foldchanges,pathway.id=pid,species="hsa"))
Info: Downloading xml files for hsa04614, 1/1 pathways.. Warning: Download of hsa04614 xml file failed! This pathway may not exist!
Info: Downloading png files for hsa04614, 1/1 pathways.. Warning: Download of hsa04614 png file failed! This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04614 skipped! 'select()' returned 1:1 mapping between keys and columns
Info: Working in directory C:/Users/leena/OneDrive/Desktop/RNA Seq-TaMXene-Weiang-May2022 Info: Writing image file hsa04142.pathview.png Info: some node width is different from others, and hence adjusted!
Info: Downloading xml files for hsa04145, 1/1 pathways.. Warning: Download of hsa04145 xml file failed! This pathway may not exist!
Info: Downloading png files for hsa04145, 1/1 pathways.. Warning: Download of hsa04145 png file failed! This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04145 skipped! Couldn't find end of Start Tag relation line 704 Premature end of data in tag pathway line 4 Warning: Parsing ./hsa04141.xml file failed, please check the file!
Info: Downloading xml files for hsa00980, 1/1 pathways.. Warning: Download of hsa00980 xml file failed! This pathway may not exist!
Info: Downloading png files for hsa00980, 1/1 pathways.. Warning: Download of hsa00980 png file failed! This pathway may not exist! Warning: Failed to download KEGG xml/png files, hsa00980 skipped!
Warning messages: 1: In download.file(xml.url, xml.target, quiet = T) : URL 'https://rest.kegg.jp/get/hsa04614/kgml': status was 'Failure when receiving data from the peer' 2: In download.file(xml.url, xml.target, quiet = T) : URL 'https://rest.kegg.jp/get/hsa04145/kgml': status was 'Failure when receiving data from the peer' 3: In download.file(xml.url, xml.target, quiet = T) : URL 'https://rest.kegg.jp/get/hsa00980/kgml': status was 'Failure when receiving data from the peer'
Cross-posted: https://support.bioconductor.org/p/9144648/