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  • could not find function "DESeqDataSetFromMatrix"

    Hi

    I am trying to use DESeq2 for differential expression analysis.
    Everything goes fine:
    DESeq2 is installed in R-

    Code:
    .......
    installing to /usr/local/lib/R/site-library/DESeq2/libs
    ** R
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
    * DONE (DESeq2)
    but upon using DESeqDataSetFromMatrix, I get the error:

    Code:
    Error: could not find function "DESeqDataSetFromMatrix"
    The command that I am giving is:

    Code:
    Data1<-DESeqDataSetFromMatrix(countData=countData,colData=colData, design=~condition)
    Any clues/help shall be much appreciated.

    Thanks.
    M

  • #2
    You forgot to:

    Code:
    library(DESeq2)
    Just because it's installed doesn't mean it's loaded.

    Comment


    • #3
      Hi dpryan

      Yes, I already did library(DESeq2).
      But now I figured out the problem, which was due to RStudio.
      It is working fine in the shell.
      However, I thank you very much for taking time out and pointing out these noob mistakes.

      Best
      M

      Comment

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