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  • What do the numbers mean in these RNA-Seq gene/transcript TPM files?

    From the link https://gtexportal.org/home/datasets, under V7, I'm trying to do R/Python analyses on the Gene TPM and Transcript TPM files. But in these files (and to open them I had to use Universal Viewer since the files are too large to view with an app like NotePad), I'm seeing a bunch of ID's for samples (i.e. GTEX-1117F-0226-SM-5GZZ7), followed by transcript ID's like ENSG00000223972.4, and then a bunch of numbers like 0.02865 (and they take up like 99% of the large files). Can someone help me decipher what the numbers mean, please? And are the numbers supposed to be assigned to a specific sample ID? (The amount of letters far exceed the amount of samples, btw). I tried opening these files as tables in R but I do not think R is categorizing the contents of the file correctly.

    For context, I am planning to match males with females for sex comparison but in order to do that, I need to get R to categorize everything correctly. (I know that females have "F" where ####-#####-####-#x-##### where x is and males have "M").

  • #2
    Hey Macromind101

    Those numbers represent the TPM (Transcripts Per Million) for each sample. So the numbers are not assigned to a specific sample ID directly, instead, each number corresponds to the expression level of a specific gene or transcript in a specific sample.



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