No chromosome Y data for genocluster and LRR/BAF- Affy Axiom data

[Melb1]

Hi there

I am generating genocluster followed by LogRR/BAF on Axiom PMDA data. It working for all chromosomes but not for Y and we are particularly interested in Chr Y.
The pfb file has annotation for all chr Y probes ?

any idea why this is happening?

[kaichop]

You need to generate PFB file yourself, from your own array data.

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On Tue, Nov 19, 2019 at 3:29 PM Melb1 ***@***.***> wrote: Hi there I am generating genocluster followed by LogRR/BAF on Axiom PMDA data. It working for all chromosomes but not for Y and we are particularly interested in Chr Y. The pfb file has annotation for all chr Y probes ? any idea why this is happening? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#50?email_source=notifications&email_token=ABNG3ODEJ6ZRNH5JHO3AS7LQUREDVA5CNFSM4JPI6XKKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H2OU2UQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OFEIRXJPCPD4T2QGQLQUREDVANCNFSM4JPI6XKA> .

[Melb1]

How i can generate the pfb file?

[kaichop]

compile_pfb.pl can be used

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On Tue, Nov 19, 2019 at 3:43 PM Melb1 ***@***.***> wrote: How i can generate the pfb file? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50?email_source=notifications&email_token=ABNG3OGZPNGUML4CSZ2IQ7DQURFV7A5CNFSM4JPI6XKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEPV7EY#issuecomment-555704211>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OGTB7RCMBIGA2MGL2TQURFV7ANCNFSM4JPI6XKA> .

[Melb1]

can you please provide me a link where i can find the detail of compile_pfb.pl,

[kaichop]

You are asking the question on the github repository that hosted PennCNV. https://github.com/WGLab/PennCNV

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On Tue, Nov 19, 2019 at 3:51 PM Melb1 ***@***.***> wrote: can you please provide me a link where i can find the detail of compile_pfb.pl, — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50?email_source=notifications&email_token=ABNG3OH3WIHVUS3VMEUCRQDQURGTRA5CNFSM4JPI6XKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEPWYYA#issuecomment-555707488>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OEWUGLGPHP6IM522VTQURGTRANCNFSM4JPI6XKA> .

[Melb1]

Thanks, i know about github repository for compile_pfb.pl, but need to know the example to use it, like what input files etc.

[Melb1]

Anyother issue is compile.pfb aspet B allele freq file and I do not have chr Y probes in B allele freq files?

[kaichop]

Just run it and it will tell you how to use it, like any other command in penncnv.

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On Tue, Nov 19, 2019 at 3:59 PM Melb1 ***@***.***> wrote: Thanks, i know about github repository for compile_pfb.pl, but need to know the example to use it, like what input files etc. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50?email_source=notifications&email_token=ABNG3ODMPNIW3TVOCCCGDCDQURHTBA5CNFSM4JPI6XKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEPXXKY#issuecomment-555711403>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OAHTQCSVZFKACEWHYDQURHTBANCNFSM4JPI6XKA> .

[kaichop]

you should first learn how to use penncnv, understand all the basics such as how to run a command and how to interpret results, there are online tutorials that give step by step instructions. Do not use GitHub Issue for asking questions.

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On Tue, Nov 19, 2019 at 4:20 PM Melb1 ***@***.***> wrote: Anyother issue is compile.pfb aspet B allele freq file and I do not have chr Y probes in B allele freq files? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50?email_source=notifications&email_token=ABNG3OHQM7CHIYJ3OB3T54DQURKADA5CNFSM4JPI6XKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEPZ3YA#issuecomment-555720160>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OC6OKL7GA7OLNMZUZTQURKADANCNFSM4JPI6XKA> .

[Melb1]

okay thanks, sorry for confusion but it says aspect B allele freq file and I do not have chr Y probes in B allele freq files?

[kaichop]

What does " aspect B allele freq file" mean? I do not have any idea. What is "it" in "it says"? Did you check with whoever provided you with the data why there is no chrY probe in BAF file, and why you want to have chrY CNV calls from a file that has no chrY markers? It could be that only CN markers are provided in chrY but even if so, these markers should still be in BAF file typically. Again, read the tutorials, FAQs, instructions, etc, and run the example commands first, to get some basic understanding of PennCNV, before digging into more advanced topics.

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On Tue, Nov 19, 2019 at 4:34 PM Melb1 ***@***.***> wrote: okay thanks, sorry for confusion but it says aspect B allele freq file and I do not have chr Y probes in B allele freq files? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50?email_source=notifications&email_token=ABNG3OD2NFUX7BDF3RS3JPDQURLXDA5CNFSM4JPI6XKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEP3JTA#issuecomment-555726028>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OAD3LSTNCIDDZF45JDQURLXDANCNFSM4JPI6XKA> .