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  • Script for FPKM with Deseq2 - help

    Hello to all.
    I'm new in R, but I'm working with RNA-seq data for a work in a course.
    Specifically, I have a count matrix similar to that:

    gene sample1 sample2 sample3 sample4 gene_length(nt)
    A 10 100 1000 10000 5000
    B 20 200 2000 20000 5000
    C 30 300 3000 30000 5000
    D 1 5 10 15 5000

    I maked a Perl script to calculate FPKM, but now also I need to make other in R.
    I read that DESEQ2 have functions to obtain fpkm.
    But, at the moment for me has been impossible to generate a script for that.

    I've only done this, but have error ("Error in all_dims[, 1L]"):
    -----------------------------------------------

    library(DESeq2)

    data <- read.delim(file = "prueba.tab",header = TRUE,
    sep = "\t", stringsAsFactors = FALSE)

    se <- SummarizedExperiment(list(counts=data), colData=DataFrame(sample=1:4))
    dds <- DESeqDataSet(se, ~ 1)

    fpkm(dds)

    -----------------------------------------------

    Someone can help me with that?

    Thanks for all!

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