how to start normalization
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Entering edit mode
@raghavaraghava049-16686
Last seen 3.2 years ago


Loading required package: Biobase
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    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1   2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
>  system.file
function (..., package = "base", lib.loc = NULL, mustWork = FALSE) 
{
    if (nargs() == 0L) 
        return(file.path(.Library, "base"))
    if (length(package) != 1L) 
        stop("'package' must be of length 1")
    packagePath <- find.package(package, lib.loc, quiet = TRUE)
    ans <- if (length(packagePath)) {
        FILES <- file.path(packagePath, ...)
        present <- file.exists(FILES)
        if (any(present)) 
            FILES[present]
        else ""
    }
    else ""
    if (mustWork && identical(ans, "")) 
        stop("no file found")
    ans
}
<bytecode: 0x000000001abf07e0>
<environment: namespace:base>
>  datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" ) 
> datafile = system.file
> system.file
function (..., package = "base", lib.loc = NULL, mustWork = FALSE) 
{
    if (nargs() == 0L) 
        return(file.path(.Library, "base"))
    if (length(package) != 1L) 
        stop("'package' must be of length 1")
    packagePath <- find.package(package, lib.loc, quiet = TRUE)
    ans <- if (length(packagePath)) {
        FILES <- file.path(packagePath, ...)
        present <- file.exists(FILES)
        if (any(present)) 
            FILES[present]
        else ""
    }
    else ""
    if (mustWork && identical(ans, "")) 
        stop("no file found")
    ans
}
<bytecode: 0x000000001abf07e0>
<environment: namespace:base>
> datafile = system.file( "extdata/ datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" ) 
Error: unexpected symbol in "datafile = system.file( "extdata/ datafile = system.file( "extdata"
> datafile = system.file( "extdata/GSE54167_Non-normalized_data.txt", package="DESeq" )


> browseVignettes("DESeq")
starting httpd help server ... done

deseq • 366 views
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Entering edit mode

Just posting a bunch of code isn't likely to get people to try to answer your question. What exactly are you trying to do?

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