Hey,
I was just going through the data and I noticed that: 'H1793', 'HF2597', 'HSTS', 'KRJ1', 'LNCAP', and 'U87' are not mapped within CCLE and other databases. Is this intentional? Are the files using non-CCLE names? For example, U87 = U87MG?
sean
Created by Sean McCurdy seanmccrdy @efd2115 thanks for the reply and some ideas. Appreciate it! Our database is independent of CCLE and so the cell-line overlap is not perfect (this is the "cost of doing" business for most integrative analysis). You have correctly identified the non-CCLE lines except for: H1793, U87 and LNCAP which are: NCIH1793, U87MG and LNCAPCLONE...(I can't remember the exact lncap name off-hand) w/n the CCLE database.
This has not been an issue in the past challenge because most participants chose to average the cell-lines to give a pan-cancer signature. Individual matching of lines to other data-sets is an alternative but it has the disadvantage of discarding data for which CCLE-lines don't exit.
Hi Sean,
I've cced @efd2115 who is probably best poised to answer this question.
Best,
Robert