Omics Academy

Some recent posts reminded me that it might be useful for us to review the options for converting between genome coordinate systems. This comes up in several contexts. Probably the most common is that you have some coordinates for a particular version of a reference genome and you want to determine the corresponding coordinates on a different version of the reference genome for that species. For example, you have a bed file with exon coordinates for human build GRC36 (hg18) and wish to update to GRC37 (hg19). By the way, for a nice summary of genome versions and their release names refer to the  Assembly Releases and Versions FAQ Or perhaps you have coordinates of a gene and wish to determine the corresponding coordinates in another species. For example, you have coordinates of a gene in human hg19 and wish to determine corresponding coordinates in mouse mm10. Finally you may wish to convert coordinates between coordinate systems within a single assembly. For example, you have t

Dear Jack, The thing to understand is that terms like FDR and q-value were defined in specific ways by their original inventors but are used in more generic ways by later researchers who adapt, modify or use the ideas. The term "false discovery rate (FDR)" was created by Benjamini and Hochberg in their 1995 paper. They gave a particular definition of what they meant by FDR. Their procedure accepted or rejected hypotheses, but did not produce adjusted p-values. Benjamini and Yekutieli presented another more conservative algorithm to control the FDR in a 2001 paper. Same definition of FDR, but a different algorithm. In 2002, I re-interpreted the Benjamini and Hochberg (BH) and Benjamini and Yekutieli (BY) procedures in terms of adjusted p-values. I implemented the resulting algorithms in the function p.adjust() in the stats package, and used them in the limma package, and this lead to the concept of an FDR adjusted p-value. The terminology used by the p.adj