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4.0 years ago
jabbari.parnian
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30
Hi everyone,
I have a table of gene expression levels of a single cell RNA-seq experiment and the expression values. The values for each gene vary between 0 and 15.923 for different genes among different cells. How can I know if the table provides fpkm or tpm?
Thanks,
Could the sum of all genes in the table, per sample (sum of rows or columns, depending on the layout), be in TPM the same for all samples, but FPKM be different between the samples?
Could be. Still, with an assay as variable and batch-confounded as scRNA-seq, I would not start guessing. I'd get exact information from the creator of that table, and if not available then start over from raw counts. in the end you only add up uncertainties.
By looking at the methods text or asking the guy who create it.
From the numbers you can also tell that they are log transformed.