Dear all,

Hi! I wonder, for aCGH data analysis, what is the threshold cutoff values or

criteria used to call gain, amplification, loss, and deletions? I know some
might use arbitrary numbers as thresholds but I am curious about whether
there is a better way to take into account case by case.

In case, all my data are cancer samples without normal samples as
references,
what could be the best way to infer the threshold values to call
aberrations? Shall
I take the mean copy number of all probes across all samples to use it as
the backgroun
or if I have a target gene, and I can just take the mean copy number of the
probes against
this target gene across all samples?

Thank you so much for your help in advance!

Sincerely,
     Allen

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