[Reposting from an approved email address]
Hi Benilton,
The locus level (total) CN ratios passed to CBS is simply the
log2(T/R), where 'T' is the total CN signal (no ratio) for sample T
("tumor" say) and 'R' is ditto for the reference used to standardize
(aka "normalize" by some books). Typically, 'R' is either a matched
normal or a global reference (e.g. median across all available 'T':s).
In the end of the day, if you see global biases in mean/median levels
after CBS, then that is already there in the log2(T/R) ratios, or
equivalently, in the T/R ratios. It's not clear what type of
reference 'R' you use, and what preprocessing, but the
genome-wide/global average - median(log2(T/R)) - is basically assumed
to be zero at the point you pass it to CBS.
>From your figure it also not clear what the scale of your color scale
is; could it be that threshold for "white" is so small that even the
teeniest bias in median(log2(T/R)) shows up? Looking the the
ChromosomeExplorer plots helps here.
You could extract the T's and R's manually and run it trough
DNAcopy::segment() (or PSCBS::segmentByCBS()) manually to see if you
can do a better centralization of the log2(T/R) signals.
Hope this helps
Henrik
On May 19, 2015 10:27 PM, "Benilton Carvalho" <beniltoncarva...@gmail.com>
wrote:
>
> Hi everyone,
>
> if you check the image at:
>
>
https://dl.dropboxusercontent.com/u/83643/Screen%20Shot%202015-05-20%20at%201.50.50%20AM.png
>
> you'll see segmentation results for a few human samples across multiple
chromosomes. This was achieved via CBS (under the aroma framework,
therefore CbsModel).
>
> A few samples show constant gain/loss levels across several chrs and
that's quite unlikely, suggesting the possibility of an issue with the
sample-specific intensity levels. My question: is there a simple solution
under the aroma framework to adjust for that?
>
> thanks, b
>
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