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Old 08-06-2018, 07:00 PM   #1
Name_less_
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Location: Chile

Join Date: Oct 2014
Posts: 12
Default 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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