I see. Thanks a lot,
Sean
On Tue, Aug 6, 2013 at 8:05 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> Hi.
>
> On Tue, Aug 6, 2013 at 12:31 PM, ying chen wrote:
> > Hi Henrik,
> >
> >
> > Sorry I have one more question to bug you. The urls in the df (by df <-
> > readDataFra
Hi.
On Tue, Aug 6, 2013 at 12:31 PM, ying chen wrote:
> Hi Henrik,
>
>
> Sorry I have one more question to bug you. The urls in the df (by df <-
> readDataFrame(db);) point to UCSCgenome browser with NCBI36/hg18 assembly. I
> looked at the http://www.aroma-project.org/chipTypes/GenomeWideSNP_6 pa
Hi Henrik,
Sorry I have one more question to bug you. The urls in the df (by df <-
readDataFrame(db);) point to UCSCgenome browser with NCBI36/hg18 assembly.
I looked at the http://www.aroma-project.org/chipTypes/GenomeWideSNP_6 page
resource part, the SNP6 chip type files are listed as based on
On Thu, Aug 1, 2013 at 6:37 PM, ying chen wrote:
> Hi Henrik,
>
> Thanks a lot for the help.
>
> For sm <- CbsModel(dsTR, ref=dfR, tags="HapMapRef"), you mean sm <-
> CbsModel(dsT, ref=dfR, tags="HapMapRef"), right?
Correct, I meant:
sm <- CbsModel(dsT, ref=dfR, tags="HapMapRef")
/H
>
> Thanks
Hi Henrik,
Thanks a lot for the help.
For sm <- CbsModel(dsTR, ref=dfR, tags="HapMapRef"), you mean sm <-
CbsModel(dsT, ref=dfR, tags="HapMapRef"), right?
Thanks,
Sean
On Thu, Aug 1, 2013 at 6:00 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> On Mon, Jul 29, 2013 at 7:4
On Mon, Jul 29, 2013 at 7:45 PM, ying chen wrote:
> Hi Henrik,
> Thanks a lot for the help!
> Sorry I have more questions. I am following "How to: Calculate total copy
> number ratios from total (non-polymorphic) signals" and "Vignette: Total
> copy-number segmentation (non-paired CBS)", but I am
Sorry, one more question regarding CBS. During
fit(sm, verbose=-10)
Building tuple of reference sets...
Type of reference: median
No reference available.
Calculating average copy-number signals...
Retrieving average unit signals across 291 arrays...
..
I tho
Sorry, one more question regarding CBS. During
fit(sm, verbose=-10)
Building tuple of reference sets...
Type of reference: median
No reference available.
Calculating average copy-number signals...
Retrieving average unit signals across 291 arrays...
..
On Thu, Aug 1, 2013 at 10:53 AM, y
Hi Henrik,
I tried method I mentioned above. But I got an error message when running
fit(sm, verbose=-10).
Array #1 ('321T') of 291 on chromosome 1...
Error in UseMethod("getChecksum") :
no applicable method for 'getChecksum' applied to an object of class
"list"
What did I do wrong?
Than
Hi Henrik,
Thanks a lot for the help!
Sorry I have more questions. I am following "How to: Calculate total copy
number ratios from total (non-polymorphic) signals" and "Vignette: Total
copy-number segmentation (non-paired CBS)", but I am not sure if I do it
correctly.
I have two SNP6 datasets Tumor
Hi.
On Fri, Jul 26, 2013 at 8:02 AM, sean nj wrote:
> Hi guys,
>
> I have a question regarding how to calculate raw copy numbers using common
> reference instead of average of all samples of the study. Basically I want
> to use average of HapMap270 samples as reference for all further copy number
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