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!
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!