Question: how to start normalization
0
gravatar for raghavaraghava049
15 months ago by
raghavaraghava0490 wrote:


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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 • 234 views
ADD COMMENTlink written 15 months ago by raghavaraghava0490

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?

ADD REPLYlink written 15 months ago by James W. MacDonald51k
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