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.
I'm assuming you're looking at a file that ends with "...v7_RNASeQCv1.1.8_gene_tpm.gct", which has the gene or transcript-level TPM values. Note that the file contains 2 rows prior to the actual header with the sample IDs, which is probably why R wasn't reading it into a data.frame appropriately. If you're using read.table() function to read the file into R, you can use the "skip" argument to skip the first 2 lines.
As for your main question, the numbers filling most of the file are the TPM values, which are the normalized expression measurements for the various genes/transcripts in the given samples. TPM stands for "Transcripts Per kilobase Million" and it gives a measure of expression that normalizes for both gene/transcript length and overall read depth (i.e., total reads from the sequencing), in that specific order. TPM has emerged as a preferred normalized metric because TPM values have a consistent meaning across both samples and genes. Here is a short explainer video on TPM vs other common normalized metrics: https://youtu.be/TTUrtCY2k-w
I'm not sure what letters you mean when you say "The amount of letters far exceed the amount of samples." But let me briefly note that there are more samples than subjects in the dataset because individual subjects typically have samples from several different organs/tissue types.
These files are gene expression matrices. They contain samples as columns, rows as gene names, and gene expression values as TPM.
These values you see like such: "GTEX-1117F-0226-SM-5GZZ7" are sample identifiers. There are also meta data files, like so "GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt." which contain rows as those sample identifiers and columns contain meta data about each sample like tissue type, nucleic acid and library prep QC/QA info, and then sequencing QC metrics like read length, depth, and coverage.
GTEX-1117F-0226-SM-5GZZ7 is the sample ID and the ENSG00000223972.4 refers to the gene symbol according to the HUGO gene nomenclature. The numbers you are referring to are gene expression values. TPM (Transcripts Per Million) is a normalization method that has been used to scale these gene expression values so that it is possible to make the expression of genes comparable between samples.
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