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Hi, I am new to bioconductor. Is there a good package/work flow that
does copy
number/LOH analysis for Affy 100K chips, starting from CEL files? I
have 100K
data from ~ 30 tumor samples; and I plan to download 100K trios data
(90 healthy
individuals) as normal references from Affymetrix website. Do I really
need
normal references for copy number/LOH analysis? Cheng Li of dChip had
a paper in
PLoS Computational Biology 2006 describing that dChip can infer LOH
from
unpaired tumor samples without using normal references, is there a
package in
bioconductor that can do this?
Thank you.
John
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