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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Normal/Neutral copy numbers (cn=2)? -Axiom_array(PMRA) #19

Closed lalamot closed 6 years ago

lalamot commented 6 years ago

RE: PennCNV-affy calling - axiom PMRA array data

Kindly, I just successfully ran PennCNV-1.0.3 "detect_cnv.pl" to call cnvs. I do however noticed that the generated copy numbers are either cn=1,0,or 3 and no 2(neutral/normal). Kindly how or what flag do I need to invoke in order get all segments including the neutral/normal ones?

Thank you

kaichop commented 6 years ago

If it is not shown in results, then it is neutral copy number.

On Thu, Nov 30, 2017 at 6:48 PM, lalamot notifications@github.com wrote:

RE: PennCNV-affy calling - axiom PMRA array data

Kindly, I just successfully ran PennCNV-1.0.3 "detect_cnv.pl" to call cnvs. I do however noticed that the generated copy numbers are either cn=1,0,or 3 and no 2(neutral/normal). Kindly how or what flag do I need to invoke in order get all segments including the neutral/normal ones?

Thank you

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lalamot commented 6 years ago

Indeed helpful, thank you so much for the prompt response, it validates our assumption. Thank you

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, November 30, 2017 6:49 PM To: WGLab/PennCNV PennCNV@noreply.github.com Cc: Lala Motlhabi (non-Celgene) lmotlhabi@celgene.com; Author author@noreply.github.com Subject: Re: [WGLab/PennCNV] Normal/Neutral copy numbers (cn=2)? -Axiom_array(PMRA) (#19)

If it is not shown in results, then it is neutral copy number.

On Thu, Nov 30, 2017 at 6:48 PM, lalamot notifications@github.com wrote:

RE: PennCNV-affy calling - axiom PMRA array data

Kindly, I just successfully ran PennCNV-1.0.3 "detect_cnv.pl" to call cnvs. I do however noticed that the generated copy numbers are either cn=1,0,or 3 and no 2(neutral/normal). Kindly how or what flag do I need to invoke in order get all segments including the neutral/normal ones?

Thank you

— 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/19, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuDq7jbMhIQGZIQ6V60IYxhDEpGs0ks5s7z6xgaJpZM4QxqBi .

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