Dear aroma community,
We are trying to do paired CBS analysis on some Affy SNP 6.0 data
using the R package "PSCBS", but not sure how to extract the total CN
and BAF values from the raw array files (.CEL) into the needed format
(pasted below). It seems aroma.affymetrix has some relevant functions
but there are few examples to follow. Could someone provide some
sample code on this? Thanks!
chromosome position CT betaT CN
betaN
SNP_A-8575125 1 554484 1.8778996 0.06460427 1.8856720
0.1161352
SNP_A-8575115 1 554636 0.1659543 0.64621653 0.2282602
0.6919347
SNP_A-8575371 1 557616 2.1193934 0.82567971 2.3405546
0.8425635
SNP_A-8709646 1 711153 1.3974123 0.25975011 2.2465997
0.1765471
CT: total tumor copy number
betaT: tumor allele B fractions (BAFs)
CN: total matched normal copy number
betaN: matched normal BAFs
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