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Converting between CNV Algorithm results (PICNIC v GISTIC)

Hello,

I am working with a tool that uses CNV as part of its analysis and was built originally around TCGA data, so its calculations are based on the Birdsuite/GISTIC pipeline. I want to use a dataset from another group, but they used PICNIC to calculate their CNV values and I am running into issues because the outputs are on a different scale. I'm wondering if anyone has run into this before and knows of a way (or a package) to convert between the two without having to get the raw files and run them through Birdsuite/GISTIC from scratch.

Thanks!

microarray cnv picnic gistic snp6
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updated by Ahmad • Ahmad • written by sunnyjjones • sunnyjjones

Apologies for what may probably be a misuse of the comments section, but I came across a similar problem and I was wondering whether you may have made some progress with yours? I ran into issues as well due to the different scales used in the PICNIC and GISTIC pipeline.

I know what the scales meant in the GISTIC pipeline but I'm having difficulty interpreting the scales used in PICNIC. The g-score in GISTIC means: 0 : normal (no amplification or deletion) -1 : heterozygous or hemizygous deletion -2 : homozygous deletion 1 : 1 copy amplification 2 : high copy amplification (> 1 copy amplification)

Thank you!!!

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written by Ahmad • Ahmad

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