I feel like the question might have been asked already, but I could not find it. So please bear with me. I am trying to use TCGA gene expression data for my project, and noticed that the sums of TPM values for tumor samples are not the same, not even close. This seems odd to me since I think, for each sample, the sum of TPM should be 1,000,000 by definition (or at least very close to it). I guess I must be missing something obvious here, but could not figure it out. Any help would be very much appreciated.
ps. if I need to compare the expression of a gene across samples, do I need to normalize it for each sample by its sum of TPM?
Best regards,
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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