I mapped the Human Ensembl IDs using Biomart package in R. It gave me a one-to-one mapping for Ensembl gene ID to External gene ID. Is this Ensembl gene ID different from Original Ensembl IDs which I had initially in my files?
The original Ensembl IDs had a decimal after the number ends like "ENSG00000280109.1" but on the same hand, its corresponding Ensembl gene ID ("ENSG00000280109") is decimal free which I gave as values in Biomart code. Please explain what is the difference between these two?
And secondly, UCSC Xena browser gives us a list of Ensembl IDs and their corresponding mapped gene symbols, but there are many cases in which the same gene corresponds to different Ensembl IDs.
Which one should I trust? Mapping via Biomart or the mapping file provided by XENA itself.
On what criteria is Biomart assigning a single gene to each Ensembl gene ID/original Ensembl IDs whereas UCSC Xena provides different Ensembl IDs corresponding to the same gene.