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  • Why could I not find "kegg.gsets" function in gage package?

    Hi bigmw,
    I could not find the function of "kegg.gsets" in gage package. Do you have any idea about it?
    Was it because I used version 2. 12.0 instead of 2.11.3?
    > library(gage)
    > ?kegg.gsets
    No documentation for ‘kegg.gsets’ in specified packages and libraries:
    you could try ‘??kegg.gsets’

    Thanks a lot!!

    Richard
    Last edited by wmseq; 11-25-2013, 12:53 PM.

  • #2
    kegg.gsets is a new function introduced into gage since Bioconductor 2.13 (gage version >= 2.12.0).
    Make sure you install the current release version here:
    GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

    Comment


    • #3
      Thanks, bigmw!
      I am sure I installed it from Bioconducto 2.13.
      The commands I used are as follows:
      source("http://bioconductor.org/biocLite.R")
      biocLite("gage")

      Comment


      • #4
        The the package version biocLite() installs depends on your R/Bioconductor version. To install the current release of bioc packages like gage, you have to make sure your R/Bioconductor version is or newer than 3.0/2.13. To check the status/versions of your bioc packages:
        If you are sure you have R version 3.0 or later:
        library(BiocInstaller)
        biocValid()

        If you are not sure, do:
        sessionInfo()

        I would expect you see outdated R/Bioconductor (and package) versions from above output. To install or update your R/Bioconductor, please check:
        The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

        Comment


        • #5
          Hi bigmw,
          I have solved the problem. It was because some files in a local directory could not be updated automatically, so that they have to be removed by hand, and than update R.

          Now, I can find "kegg.gsets" function, but when I ran the following command, I got another error message.

          > kg.ame=kegg.gsets("ame")
          Error in korg[ridx, coln] : subscript out of bounds

          Do you have any idea on its fixing?

          Thanks!

          Richard

          Comment


          • #6
            The code I give you has been tested across multiple platforms. Below is what I got on my computers. No sure what happened on your side.
            You seem to have many odd problems with your computer based on your previous questions/notes. I would suggest you either find another computer or clean up your system (if you can) and resintall the updated R/Bioconductor, gage, pathview and other package from scratch. This will make your work much easier.

            > kg.ame=kegg.gsets("ame")
            > lapply(kg.ame, head, 3)
            $kg.sets
            $kg.sets$`ame00010 Glycolysis / Gluconeogenesis`
            [1] "408559" "408654" "409624" "409773" "410122" "411140" "411188" "411576" "411897" "412362" "412522" "412843" "413924"
            [14] "550687" "550785" "551005" "551039" "551103" "551154" "551631" "552007" "552086" "552678" "552736" "724724" "725455"
            [27] "726117" "726225" "727153" "727456"

            $kg.sets$`ame00020 Citrate cycle (TCA cycle)`


            $sigmet.idx
            [1] 76 82 83

            $sig.idx
            [1] 76 82 83

            $met.idx
            [1] 1 2 3

            $dise.idx
            integer(0)

            Comment


            • #7
              Thanks a lot, bigmw!
              I will consult a computer guy to do it.

              Comment


              • #8
                One thing you may also consider is to double check that gage has readlly been updated and successfully reloaded. You may want to restart an R session, and do:
                library(gage)
                kg.ame=kegg.gsets("ame")

                If the same problem still persist, do:
                sessionInfo()

                and post the output here.

                Comment

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