Tumor and Normal CEL files?

[vymao]

I am following this guide (http://penncnv.openbioinformatics.org/en/latest/user-guide/affy/) in order to generate the lrr_baf.txt file following the first set of instructions. I am a bit confused on how to follow this guide if we have tumor and normal CEL files. Should we be putting all the CEL files we have (tumor and normal) into a single cel_files.txt file, or do we run separate analyses somehow?

[kaichop]

You can put them into the same file for analysis, to ensure a fair comparison with less batch effects.

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On Wed, Jul 22, 2020 at 12:28 PM Victor Mao ***@***.***> wrote: I am following this guide ( http://penncnv.openbioinformatics.org/en/latest/user-guide/affy/) in order to generate the lrr_baf.txt file following the first set of instructions. I am a bit confused on how to follow this guide if we have tumor and normal CEL files. Should we be putting all the CEL files we have (tumor and normal) into a single cel_files.txt file, or do we run separate analyses somehow? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#59>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OEMWEHD5YWSPNXPZZLR44HUHANCNFSM4PE4FYZQ> .