I'm having difficulty normalizing my data.
I was searching for transposable elements in my genome, and after this step, I made counts of reads in some transcripts. I produced something like this:
head(table_tissues_filtered_TE)
Lengths ova testes lobe retina suckers brain1 brain2 skin stage
Simple_repeat_80 134 58 77 48 69 115 137 131 195 75
tRNA_1 59 0 14 12 1 19 12 14 21 104
Simple_repeat_87 26 1 33 12 3 15 24 21 19 180
Simple_repeat_114 22 0 0 0 1 0 0 0 2 7
Simple_repeat_115 30 0 0 0 0 0 0 0 0 1
Simple_repeat_123 22 2 3 317 45 13 652 651 15 21
axial gland viscera
Simple_repeat_80 99 35 557
tRNA_1 9 0 3
Simple_repeat_87 9 0 4
Simple_repeat_114 0 204 0
Simple_repeat_115 0 42 0
Simple_repeat_123 333 5 4
where Lengths are the Length of each elements (simple repeats, etc), and the other columns indicate the reads counted with FeatureCounts. I have another table with the number of reads for each tissue:
head(reads_table)
ova testes lobe retina suckers brain1 brain2 skin stage axial
522444 310243 226146 102307 126055 489389 668243 372728 262536 233754
gland viscera
24817 25689
I would like to do an RPkM analysis to normalize the data using R, but I don't know exactly how to do it. Can anyone can help me? thank you!!!
