Open ghost opened 4 years ago
May I ask in function findDAR, is there any normalization being done? thanks!!
Hi Rong,
There is no normalization down prior to the test. It starts with raw read count.
Best
On Oct 17, 2019, at 12:43 PM, rong923 notifications@github.com wrote:
when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.
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Hi Thanks so much for your reply. Is there normalization during the test? On Thu, Oct 24, 2019 at 5:35 AM Rongxin Fang notifications@github.com wrote:
Hi Rong,
There is no normalization down prior to the test. It starts with raw read count.
Best
On Oct 17, 2019, at 12:43 PM, rong923 notifications@github.com wrote:
when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/r3fang/SnapATAC/issues/117?email_source=notifications&email_token=ABT6GG6O2QQNWQ4P2HPPPKDQPCI4FA5CNFSM4JB4IC32YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSQR7NA>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABT6GG64WE3VC7AF5IA7QKTQPCI4FANCNFSM4JB4IC3Q .
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Yes! It will be normalized to CPM during the test
On Oct 24, 2019, at 12:00 PM, rong923 notifications@github.com wrote:
Hi Thanks so much for your reply. Is there normalization during the test? On Thu, Oct 24, 2019 at 5:35 AM Rongxin Fang notifications@github.com wrote:
Hi Rong,
There is no normalization down prior to the test. It starts with raw read count.
Best
On Oct 17, 2019, at 12:43 PM, rong923 notifications@github.com wrote:
when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/r3fang/SnapATAC/issues/117?email_source=notifications&email_token=ABT6GG6O2QQNWQ4P2HPPPKDQPCI4FA5CNFSM4JB4IC32YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HSQR7NA>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABT6GG64WE3VC7AF5IA7QKTQPCI4FANCNFSM4JB4IC3Q .
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when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank you so much.