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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Tumor and Normal CEL files? #59

Open vymao opened 4 years ago

vymao commented 4 years ago

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 commented 4 years ago

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

On Wed, Jul 22, 2020 at 12:28 PM Victor Mao notifications@github.com 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?

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