Voom transformation of RNA seq raw counts data I have RNA seq data of raw gene counts that I want to transform for linear modelling. I am trying to voom transform, to do a weighted analysis.

Data frame: prac_count_10

gene         S1     S2    S3   S4    S5 
ENG0000456   0      1     10   145   24
ENG0000458   7      2     9    0     0
ENG0000657   76     12    56   10    2 
ENG0000689   0      0     0    3     5



Code:

prac_prac_10 &lt;- voom(prac_count_10[,2:5], design=NULL, lib.size=NULL, 
  normalize.method = "none", span = 0.5



However this doesn't give an output with the gene sample names and logCPM values. Would like an output with gene id's and logCPM values for linear modelling.

Also tried:

cpm &lt;- cpm(prac_count_10)
lcpm &lt;- cpm(prac_count_10, log=TRUE)


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Try to use DElist() function before you transform, and also make rownames first.

counts &lt;- prac_count_10[,-1]

rownames(counts) &lt;- prac_count_10[,1]

DGE1 &lt;- DGEList(counts)


And then continue with your voom...