Hi Chengyu,
On 4 February 2015 at 15:45, Chengyu Liu wrote:
> 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))?
>
yes, 23 is chromosome X and 24 is chromosome Y. Chromosome 25 is for
pseudo-autosomal
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 Chengyu,
Yes, I do have chromosome 23, 24 and 25. We are only interested in CNAs in
autosomal chromosomes so not going to include X and Y chromosomes in
further analysis.
Best,
Sam.
On 4 February 2015 at 10:31, Chengyu Liu wrote:
> Hi Sam,
>
> I would like to discuss something about cytosc
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
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output
Hi Henrik,
Thank you very much for the information and it has clarified lot of my
doubts.
Best,
Sam.
On Thursday, January 22, 2015 at 8:36:59 PM UTC+1, Henrik Bengtsson wrote:
>
> Hi guys,
>
> here are some late feedback on this discussion:
>
> * When talking about copy numbers, it is importa
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 rare
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 n
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
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
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 fr
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
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
> Cy
13 matches
Mail list logo
