PennCNV-Affy BAF and LogR position notation for SNP6 data: SNP_A vs CN

Question

[lm687]

I would be grateful if someone could point me to an explanation of the meaning of the two different types of rows in BAF and LogR of copy number profiles (output of PennCNV-Affy):

• SNP_A: I guess this refers to the (variant allele frequency) of the reference allele
• CN: I guess this stands for copy number

It's the 'CN' rows that I have difficulty understanding the meaning of, and understanding how they are generated. Thanks.

[Kevin Blighe]

Hello, can you please confirm the exact commands that you have run.

[lm687]

Hi, yes, I've ran

normalize_affy_geno_cluster.pl hapmap.genocluster quant-norm.pm-only.med-polish.expr.summary.txt -locfile affygw6.hg19.pfb -out lrr_baf_out.txt

where quant-norm.pm-only.med-polish.expr.summary.txt is created with apt-probeset-summarize.

Example output for lrr_baf_out.txt:

Name    Chr     Position        GSM996177_A891-13.CEL.Log R Ratio
SNP_A-2131660   1       1156131 0.0313
SNP_A-1967418   1       2234251 -0.0799
SNP_A-1969580   1       2329564 0.0088
SNP_A-4263484   1       2553624 0.0757
SNP_A-1978185   1       2936870 -0.1072
...
CN_434357       1       16519466        -0.5076
CN_434359       1       16520024        0.4204
CN_434362       1       16520192        0.4851
CN_435541       1       16549851        -0.0797
CN_435495       1       16535914        -0.8422
CN_435505       1       16538495        0.0796