Could be a sample annotation mistake. Wouldn't be the first time it
happened.
On Thu, Mar 5, 2015, 01:34 Chengyu Liu wrote:
> You might be right. The BAF of the normal sample is strange if the way I
> check is correct. I checked the how many bands there are. Normally there
> are three but there
Hi, it's not easy to say. My point is that you look at the normal
data, i.e. BAF (but also TCN relative to a global reference), you may
have more clues on the quality of the normal sample. If that is bad,
then then tumor-normal TCN is most likely bad too.
/Henrik
On Tue, Feb 24, 2015 at 7:42 AM,
I understand DH is defined only for heterozygous SNPs. But the total copy
number estimates look ok. Do you think I need to discard this sample or not
when I do total copy number analysis? I will discard this sample when I do
parent-specific analysis. But not sure whether I should leave this samp
Hi,
DH signals are only defined for heterozygous SNPs, so lack of DHs
indicates a problem with the matched normal BAFs (see my other email).
/Henrik
On Mon, Feb 23, 2015 at 1:53 AM, Chengyu Liu wrote:
> It is difficult for me to say whether it is failed or the normal sample is
> nose. Can you h
It is difficult to say whether it is failed or the normal sample is nose.
I am attaching two figure
On Wednesday, February 18, 2015 at 11:25:48 PM UTC+2, Henrik Bengtsson
wrote:
>
> DH is only defined from heterozygous SNPs. If you don't see any DH
> signals, that indicates that none of the SN
DH is only defined from heterozygous SNPs. If you don't see any DH
signals, that indicates that none of the SNPs where called
heterozygous. This could be an indicatation of a failed or a very
noise normal sample.
/Henrik
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run t
Additionally, the total copy number analysis shows the plot looks ok.
On Tuesday, February 17, 2015 at 12:10:44 PM UTC+2, Chengyu Liu wrote:
>
> Hi Henrik ,
>
> I have really strange result from PSCBS.
> What I did were doCRMAv2 ->extractPSCNArray->compute copy number
> -> dropSegmentationOutlie
