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How o normalize my RNA-seq dataset

Hi

I have a RNA seq datasets with three conditions (control, treatment X and Treatment Y), all triplicated. RNA sampled from brain tissue, ribosomal pulldown. I got expected counts from RSEM (STAR for alignment). I performed quantile normalization using normalizeBetweenArrays() function from Limma. I am not sure its the best way to normalize my data. You can see (image 1 )treatment Y-3 boxed area has higher gene expression than any other dataset, it looks so weird. I don't know what else I can do. Please help!

Thanks in advance

Heatmap showing the gene expression

rna-seq r alignment sequencing

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written 6.9 years ago by John

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written 6.9 years ago by John

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