I have a gene expression quantification file from TCGA that contains the following lines:ENSG00000242268.2   591.041000514ENSG00000270112.3   0.0ENSG00000167578.15  62780.6543066ENSG00000273842.1   0.0ENSG00000078237.5   36230.832883ENSG00000146083.10  189653.152706ENSG00000225275.4   0.0ENSG00000158486.12  420.761140072ENSG00000198242.12  2914738.3675ENSG00000259883.1   1632.83700531ENSG00000231981.3   0.0ENSG00000269475.2   0.0ENSG00000201788.1   0.0ENSG00000134108.11  925529.547944ENSG00000263089.1   2646.63769677ENSG00000172137.17  23162.6989867ENSG00000167700.7   291192.25157What is the .number that are added to the Gene e.g. the .2 in ENSG00000242268.2Why isn't the quantified value an integer; what does 591.041000514 mean?In case someone one wants more info about the gene LINC02082.
How to read and interpret a gene expression quantification file?
gene;normalization;identifiers;quantification
The first column contains Ensembl gene identifiers, and the suffix is a version number that can be used to track changes to the gene annotations over time. From the Ensembl Stable IDs documentation:Ensembl annotation uses a system of stable IDs that have prefixes based on the species scientific name plus the feature type, followed by a series of digits and a version e.g. ENSG00000139618.1. The version may be omitted.Following the first link you provided leads to a page with details for the file 2edcaaa7-63b4-40b4-abbe-5d7a84012e60.FPKM-UQ.txt.gz. The first thing that caught my eye about this filename was FPKM, or fragments per kilobase of exon per million reads, which is a commonly used unit of RNA expression. Since these are not raw read counts, there's no expectation that these values should be integers.The best explanation I've seen of FPKM comes from a blog post written by Harold Pimentel of kallisto and sleuth fame. From the blog post:The interpretation of FPKM is as follows: if you were to sequence this pool of RNA again, you expect to see FPKM_i fragments for each thousand bases in the feature for every N/10^6 fragments youve sequenced. Its basically just the rate of fragments per base multiplied by a big number (proportional to the number of fragments you sequenced) to make it more convenient.More generally though, even when FPKM is not the unit of expression abundance used, most quantification methods and associated units of expression will not produce integer estimates.