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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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different CNVs between two execution #40

Closed Taylor95 closed 5 years ago

Taylor95 commented 5 years ago

Hello, I have executed the detect_cnv.pl script several months ago and got CNVs based on PennCNV-1.0.4. Then now, I added the command -confidence and ran the same samples again based on PennCNV-1.0.5, but got completely different CNVs. Is this because of the version of PennCNV? or I need to set seed like in R? Thank you in advance!

kaichop commented 5 years ago

Results should be identical. There is no random seed in calling. I think you just need to make sure that the command line itself is consistent.

You could of course just re-run 1.0.4 again and check if the same results are obtained, to diagnose what was different in the command line.

On Wed, Apr 17, 2019 at 3:12 AM Taylor95 notifications@github.com wrote:

Hello, I have execute the detect_cnv.pl script several months ago and got CNVs based on PennCNV-1.0.4. Then now, I added the command -confidence and ran the same samples again based on PennCNV-1.0.5, but got completely different CNVs. Is this because of the version of PennCNV? or I need to set seed like in R? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/40, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuBnKAt-8GmDo-iDuUUE8JHsyAEnXks5vhslEgaJpZM4c0Wcv .

Taylor95 commented 5 years ago

OK, I will check carefully and try again. Thank you for answering!

————————

Yaqian Liu School of Public Health Nanjing Medical University

On 4/17/2019 20:35，Kai Wangnotifications@github.commailto:notifications@github.com wrote： Results should be identical. There is no random seed in calling. I think you just need to make sure that the command line itself is consistent.

You could of course just re-run 1.0.4 again and check if the same results are obtained, to diagnose what was different in the command line.

On Wed, Apr 17, 2019 at 3:12 AM Taylor95 notifications@github.com wrote:

Hello, I have execute the detect_cnv.pl script several months ago and got CNVs based on PennCNV-1.0.4. Then now, I added the command -confidence and ran the same samples again based on PennCNV-1.0.5, but got completely different CNVs. Is this because of the version of PennCNV? or I need to set seed like in R? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/40, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuBnKAt-8GmDo-iDuUUE8JHsyAEnXks5vhslEgaJpZM4c0Wcv .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/WGLab/PennCNV/issues/40#issuecomment-484063754, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AsJj979TjKP257daDGTBTnfXl7Qpu9xJks5vhxT4gaJpZM4c0Wcv.