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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Axiom binary to text CELS #38

Closed Vaidhy-M closed 5 years ago

Vaidhy-M commented 5 years ago

Hi there, I am having a hard time converting Axiom raw CEL files to text CELs to use it in PennCNV-Affy protocol. APT fails to do the trick as Axiom files are multi-channel. Since some users here appear to have successfully used Axiom data in PennCNV I feel like I am missing something. Please advise. Thank you for your time,

kaichop commented 5 years ago

Did you try whether ATP can directly process the axiom binary CEL file?

On Wed, Mar 13, 2019 at 1:46 PM Vaidhy-M notifications@github.com wrote:

Hi there, I am having a hard time converting Axiom raw CEL files to text CELs to use it in PennCNV-Affy protocol. APT fails to do the trick as Axiom files are multi-channel. Since some users here appear to have successfully used Axiom data in PennCNV I feel like I am missing something. Please advise. Thank you for your time,

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Vaidhy-M commented 5 years ago

apt-probeset-genotype seems to be the next step but that is not working with raw CEL files.

Vaidhy-M commented 5 years ago

Update: Turns out Axiom CELs are multi-channel and too complex to be converted to text CELs. Using apt-probeset-genotype with the correct .xml file on raw binary CELs resolved the issue.