├── 010213-01-NB_(CytoScanHD_Array).CEL
└── 010213-01-TB_(CytoScanHD_Array).CEL
On Monday, December 15, 2014 3:51:46 PM UTC+2, Chengyu Liu wrote:
Hi,
I am trying to read annotation file of CytoScanHD_Array, but somehow it
could not locate it.
I followed the tutorial
this;
csv - AffymetrixNetAffxCsvFile$byChipType(chipType)
Error in grep(pattern, basename(files0)) : invalid 'pattern' argument
I'll investigate.
/Henrik
On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu chengyu...@gmail.com
javascript: wrote:
Hi,
I am trying to read annotation file
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
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 chengyu...@gmail.com
javascript: wrote:
Hi Sam,
I would like to discuss something
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
amplified or deleted region to genes? If you
know something about it, happy to hear.
Br,
C.Y
Thanks,
Best Regards,
Sam.
On Tuesday, January 20, 2015 at 10:38:27 AM UTC+1, Chengyu Liu wrote:
Hi,
On Monday, January 19, 2015 at 3:42:59 PM UTC+2, Sam Padmanabhuni wrote:
Dear
Hi,
Please check old discussions. I remember there were discussions. I had the
same issue.
Most probably, you did not install if you were using Linux system
On Wednesday, January 21, 2015 at 3:46:49 PM UTC+2, Juanjo Lozano wrote:
Hi,
I found
Error: Package not loaded: sfit
Execution
of TCGA papers in Nature, there a fixed
threshold was used to define gain and loss. Maybe you can check that.
Br,
Br,
C.Y
Thanks,
Best Regards,
Sam.
On Tuesday, January 20, 2015 at 10:38:27 AM UTC+1, Chengyu Liu wrote:
Hi,
On Monday, January 19, 2015 at 3:42:59 PM UTC+2
Hi,
In the vignette about How to: Calculate total copy number ratios from from
total (non-polymorphic) signals, Henrik mentioned that the output of
doCRMAv2() and doASCRMAv2()are not *CN ratios *and to obtain *total CNs* (TCN),
we need to calculate the ratios for these signals relative to
available via http://aroma-project.org/howtos/
http://www.google.com/url?q=http%3A%2F%2Faroma-project.org%2Fhowtos%2Fsa=Dsntz=1usg=AFQjCNFzLVQVAza587qyuU3acW8gm18aoQ
Hope this helps
Henrik
On Thu, Jan 8, 2015 at 5:44 AM, Chengyu Liu chengyu...@gmail.com
javascript: wrote:
Hi
Hi,
I saw there was discussion about smoothing after CRMAv2 and before CBS
(https://groups.google.com/forum/#!topic/aroma-affymetrix/DUquhAMhEuY).
Henrik mentioned that function dropSegmentationOutliers in PSCBS can be
used to drop TCN outliers. I am using CytoscanHD array which includes
.
On Tuesday, January 20, 2015 at 5:01:46 PM UTC+1, Chengyu Liu wrote:
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
Hi Henrik ,
I have really strange result from PSCBS.
What I did were doCRMAv2 -extractPSCNArray-compute copy number
- dropSegmentationOutliers - segmentByPairedPSCBS- plotTracks.
But I found that one of my sample does not have any minor/major CN nor DH.
See attachment. I have checked BAF
I had script like this, I have paired samples and using allelic specif copy
number analysis.
In this vignette
(http://aroma-project.org/vignettes/PairedPSCBS-lowlevel/), manually
allele-specific copy numbers were estimated. I am thinking whether
exportTotalCnRatioSet function does the same
Following questions is that how can do if I have more samples? In this
vignette (http://aroma-project.org/vignettes/PairedPSCBS-lowlevel/
http://www.google.com/url?q=http%3A%2F%2Faroma-project.org%2Fvignettes%2FPairedPSCBS-lowlevel%2Fsa=Dsntz=1usg=AFQjCNFzc80yu6yyzSNNlmQZmIPYNymAFQ)
one pair
Hi,
I am doing allele-specific analysis using PSCBS package. I have paired
tumor-normal matched samples.
For one of the samples, i got an error which is like
at #06. lapply(names.T[8:length(names.T)], function(x) {
print(x)
y - grep(x, names(df))
if
Thanks，it is working now. I am sorry for the late reply. I was on holidays
and just back.
About ACS, UGP and UFL, are they necessary for the copy number calls?
Br,
On Monday, December 15, 2014 8:25:17 PM UTC+2, Henrik Bengtsson wrote:
On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu chengyu
Hi,
Is it necessary to update annotation files
in
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/.
It is quite old. Or I can use them without update.
Br,
C.Y
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the
Dear
When I run PSCBS segmentation and LOH calling, there was an error. Part of
error message is shown below. I do not know which sample caused this error,
which was bad. It had run for several days. Do you know what is wrong ? Do
you think the sample we (Henrik) discussed before caused this
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 SNPs
Thanks Henrik,
You are right. The sample is really noisy.
On Wednesday, February 18, 2015 at 11:23:13 PM UTC+2, Henrik Bengtsson
wrote:
I'll try to catch up with a few questions; comments below.
On Mon, Feb 9, 2015 at 3:52 AM, Chengyu Liu chengyu...@gmail.com
javascript: wrote:
Hi
(see my other email).
/Henrik
On Mon, Feb 23, 2015 at 1:53 AM, Chengyu Liu chengyu...@gmail.com
javascript: wrote:
It is difficult for me to say whether it is failed or the normal sample
is
nose. Can you have a look at these four figures ? They are from two
paired
tumor samples
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