Using dgelist function in EdgeR to calculate RPKM
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5 weeks ago
bart ▴ 20

Hi,

I'm new to RNAseq and I want to calculate rpkm values from my raw counts but I am unsure if my understanding of how to do so is correct. From what I understand, I should do the following:

df <- DGEList(counts=counts,genes=my_genes_vector,groups=my_groups_vector)) #counts should be the dataframe with all the counts, genes should be a vector with genes and groups should be a vector to which group a sample belongs (treatment vs no treatment etc)

df <- calcNormFactors(df)

RPKM <- rpkm(df, gene.length=my_gene_length_vector) #my_gene_length_vector should be a vector with all gene lengths

Is this correct?

Thanks!

rpkm edger dgelist • 152 views
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I think so. Refer to this website: https://support.bioconductor.org/p/64585/

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