Hi Sam,
I would like to discuss something about cytoscanHD array. Did you find that
when you have done preprocessing, there are chromosome 24 and 25 ?
Br,
Chengyu
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the
Thanks Sam for sharing the information.
But I dont understand, why there are chromosome 24 and 25 (autosomal
chromosome 1-22, X(23), Y(24))?
Are you using any other package than aroma.affymetrix ?
Are you interested in total copy number or allele-specific copy number
analysis ?
Now I am working
Hi,
I have tried this and works good but at the end I need the information
whether there is a gain or loss at the segment. I will use GLAD model to
get gain or loss at a segment. My samples and controls are completely
unrelated so I am little bit doubtful whether I am doing right or not.
Hi guys,
here are some late feedback on this discussion:
* When talking about copy numbers, it is important to always be very
clear and distinguish between whether we talk about normal/germline
CNs or tumor CNs. The former take integer CN levels (0, 1, 2, 3,
...), whereas for tumors we very
Hi Liu,
On Wednesday, January 21, 2015 at 4:21:04 PM UTC+1, Chengyu Liu wrote:
Hi, Sam,
No thanks, I don't need the reference papers.
On Tuesday, January 20, 2015 at 6:52:42 PM UTC+2, Sam Padmanabhuni wrote:
Hi Liu,
That is good to know some one is doing similar stuff as mine.
I
Hi, Sam,
No thanks, I don't need the reference papers.
On Tuesday, January 20, 2015 at 6:52:42 PM UTC+2, Sam Padmanabhuni wrote:
Hi Liu,
That is good to know some one is doing similar stuff as mine.
I was going to through 2-3 papers which described to get a comprehensive
list of CNVs
Hi,
On Monday, January 19, 2015 at 3:42:59 PM UTC+2, Sam Padmanabhuni wrote:
Dear AromaAffymetrix Team,
First of all, thank you very much for such a detailed vignette on how to
perform the CNV analysis.
I am Sam, a PhD student in genetics, working on CNV analysis on data from
CytoScan
Hi Liu,
That is good to know some one is doing similar stuff as mine.
I was going to through 2-3 papers which described to get a comprehensive
list of CNVs it is better to consider a CNV which is called in 2 or more
CNV calling algorithms. This is what I have observed recently in some
papers
Hi Sam,
I am doing similar stuff with you. I also need to identify regions which
are amplified or deleted. I have paired samples.
There are quite many different ways to define gain and loss of a segment.
It is a tricky question.
From the literature search, it seems best to call CNVs using
Hi,
Thanks for the clarification.
I am working on finding segments of duplication/deletion that are only
present in patients but not in controls. And my samples are non-paired.
From the literature search, it seems best to call CNVs using from different
softwares to have a comprehensive list
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