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Old 04-24-2017, 11:00 PM   #2
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Location: Sydney, Australia

Join Date: Jun 2011
Posts: 163

Of course it makes a substantial difference. TPM doesn't normalise by the length of the gene, FPKM does. Are you comparing between genes, such as by plotting the gene expression values in a heatmap? Then, you need to use FPKM. Otherwise, the heatmap may be misleading. Or, are you doing a differential expression analysis, such as calculating the fold changes of each gene between two timepoints? Then, TPM is fine, since you are comparing the same gene which has the same length between two timepoints (assuming that no alternative splicing is occurring).
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