Hi,
although sporadic, I see an increase in spam to the list. In order to
decrease the chances for this to happen, any messages from members
that just joined our group will be moderated by me. As soon as I see
that it is a valid message or if I find that someone joined the group
and did not
sessionInfo()? /H
On Wed, Sep 10, 2008 at 12:42 AM, mbaudis [EMAIL PROTECTED] wrote:
Dear all,
I have frequently bus errors when running ChromosomeExplorer for
graphics generation, and a zoom level of x64. I encountered it first
with 6.0 arrays and few cases, but also with 30 cases in the
Hi,
On Tue, Sep 16, 2008 at 5:50 AM, cruckert [EMAIL PROTECTED] wrote:
I've gone through the steps in the online vignette (Total Copy Number
Analysis (5.0 6.0)), but everytime I run process(ce) I got the
following error message:
Exception: Something is wrong with the data. Too many
What do you mean by chromosome arm information?
/Henrik
On Wed, Sep 17, 2008 at 10:25 AM, Matt [EMAIL PROTECTED] wrote:
How can I extract the chromosome arm information for a set of units.
Is there a get function that will do this?
Thanks for any help,
Matt
Hi,
I'm not sure if you narrowed down the problem or not, but I've created
a vignette showing how to stratify by different probe types in
plotDensity() and QuantileNormalization():
more so if they were done close in time. Try with
and without and search for a deletion/amplification that you can spot
by eye. I would expect that you will see a much cleaner aberration
with the extra 20 arrays.
Cheers
Henrik
Cheers
Marco
On Aug 29, 8:38 pm, Henrik Bengtsson [EMAIL
Hi.
On Tue, Sep 30, 2008 at 12:09 PM, kvenk [EMAIL PROTECTED] wrote:
Hi,
I tried to install the aroma package according to the instructions on
your website on my linux-64 machine, but got the following error:
source(http://www.braju.com/R/hbLite.R;)
Error in file(file, r, encoding =
digest_0.3.1
matrixStats_0.1.3
[10] R.rsp_0.3.4R.cache_0.1.7
R.utils_1.0.4
[13] R.oo_1.4.6 R.methodsS3_1.0.3
Best Regards
Marco
On Sep 19, 10:10 pm, Henrik Bengtsson [EMAIL PROTECTED]
wrote:
Hi.
On Fri, Sep 19, 2008 at 4:35 AM, marco [EMAIL PROTECTED] wrote
Hi.
On Tue, Oct 7, 2008 at 7:59 AM, Venkatraman E. Seshan
[EMAIL PROTECTED] wrote:
Hi Henrik:
(I am trying to get the probe-sets queried by Sty I Nsp I and
following the steps in
http://groups.google.com/group/aroma-affymetrix/web/genomewidesnp-6?version=22)
Ok, v22 of that page is
Hi Venkat,
On Thu, Oct 9, 2008 at 11:49 AM, Venkatraman Seshan [EMAIL PROTECTED] wrote:
Hi Henrik:
better from there. One warning though: If you one day decide to
hybridize with both enzymes, I doubt that you can easily mix the CEL
files from NspI-only and NspI+StyI hybs. The reference
Hi,
aroma.affymetrix v0.9.5 is now available. Please update with:
source(http://www.braju.com/R/hbLite.R;);
hbInstall(aroma.affymetrix);
The most important update in this release is a major step towards
supporting sequence annotation data and modeling of such. As a
teaser, you will soon be
Forgot one thing below:
On Mon, Oct 20, 2008 at 5:02 PM, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi,
On Mon, Oct 20, 2008 at 3:51 PM, yupu [EMAIL PROTECTED] wrote:
Hi,
I am using aroma.affymetrix to do copy number estimation on
affymetrix's SNP6.0 data.
I followed the instructions
, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Forgot one thing below:
On Mon, Oct 20, 2008 at 5:02 PM, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi,
On Mon, Oct 20, 2008 at 3:51 PM, yupu [EMAIL PROTECTED] wrote:
Hi,
I am using aroma.affymetrix to do copy number estimation on
affymetrix's
the problem.
thanks
manisha
On Jul 3, 4:14 am, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi,
what does the verbose output show? When you get theerror, what does
traceback() report?
Also, please report your sessionInfo().
/Henrik
On Thu, Jun 19, 2008 at 2:09 PM, biobee [EMAIL PROTECTED
...next reply.
On Thu, Oct 23, 2008 at 6:25 PM, Mark Robinson [EMAIL PROTECTED] wrote:
Right, just to partially answer my own question as you've already told
me about this. Sorry.
AromaCellSequenceFile object is the ticket to store the sequences for
each cell.
Yes, it stores the
Hi.
On Tue, Oct 28, 2008 at 3:52 PM, Venkat [EMAIL PROTECTED] wrote:
Thanks Henrik.
The QuantileNormalization class/method works for any Affymetrix chip type.
There are many different ways to pre-process data out there and the
two vignettes show to different ways.
I should really put up
Hi.
On Wed, Oct 29, 2008 at 1:03 PM, hailei zhang [EMAIL PROTECTED] wrote:
Hi,
I have 228 paired snp arrays, the platform is snp250k_sty. I following the
steps which is provied on the aroma website.
When I runing the step of Calibration for allelic crosstalk, I meet the
problem. After I
shows results for only one chiptype.
Is this right?
Please help! Thanks
On Oct 27, 5:33 pm, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi,
the mistake you are doing is that you tell R/aroma.affymetrix to
process both chip types, but you only have/load data for one of them.
You do
suggest
that you pick up one of the introductory books/manuals/courses on R.
/Henrik
On Oct 30, 1:12 pm, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi,
On Wed, Oct 29, 2008 at 9:54 PM, biobee [EMAIL PROTECTED] wrote:
Hi Henrik,
I ran the script as explained in the 'Paired total copy
Hi Mark,
On Fri, Oct 31, 2008 at 10:05 AM, Mark Dunning [EMAIL PROTECTED] wrote:
Hello all,
Just started using aroma, and I'm afraid I'm not getting very far :( I
think I've got a handle on how the directory structure works and can
read in some information from the cdf file correctly, but
Hi.
On Tue, Nov 18, 2008 at 8:47 AM, Bin liu [EMAIL PROTECTED] wrote:
Hi Guys,
Any clue about the questions listed below?
I tried to install on another machine which doesn't have direct link to the
internet, so I mirrored all the R2.8 and bioconductor packages on that
machine, and
:22 PM, Henrik Bengtsson wrote:
I'll let the experts on exon arrays answer this, but for clarification
this question is related to page:
http://groups.google.com/group/aroma-affymetrix/web/affymetrix-defined-transcript-clusters
/Henrik
On Tue, Nov 25, 2008 at 4:57 PM, Joe Fass [EMAIL
Hi,
On Wed, Nov 26, 2008 at 7:46 AM, mortiz [EMAIL PROTECTED] wrote:
hi everyone,
i was wondering if there is any function which gives as a result the
names of the SNPs in their rs# form?
this mapping information is available in the Affymetrix NetAffx CSV
files, which you can download from
Hi.
a comment on RmaPlm and argument 'flavor': The RmaPlm class is only
summarizing the probe signals - normalization etc are done before
RmaPlm. The summarization model is the log-additive model with probe
affinities and chip effects. The 'flavor' argument specifies which
implementation of
/annotationData/
chipTypes/MoGene-1_0-st-v1 no
print(list.files(path=path2));
[1] MoGene-1_0-st-v1,r3.cdf
Cheers,
Peter
On Nov 24, 2:59 pm, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi,
one typo by me, please retry with:
path2 - filePath(path, chipTypes, MoGene-1_0-st-v1);
[I forgot
Hi,
I just noticed the following paper:
Huntley D et al., Genome Environment Browser (GEB): a dynamic browser
for visualising high-throughput experimental data in the context of
genome features, BMC Bioinformatics, Nov 2008,
9:501doi:10.1186/1471-2105-9-501
URL:
Hi. Your versions of aroma.affymetrix and other packages are too old.
Please update. /Henrik
On Sun, Nov 30, 2008 at 11:46 PM, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
Hi,
I do paired copy number analysis with code previous working well
(with old version), this time it stopped in the PCR
Hi,
On Tue, Dec 2, 2008 at 8:06 AM, mortiz [EMAIL PROTECTED] wrote:
hi everyone,
im trying to proccess chromosomeExplorer and i get this error:
ce - ChromosomeExplorer(cbs)
process(ce, verbose=verbose)
ERROR caught in onFit.CopyNumberSegmentationModel():
simpleError in
Hi,
thanks for sharing all this.
On Tue, Dec 2, 2008 at 11:54 AM, pwhiteusa [EMAIL PROTECTED] wrote:
Hi All,
Here is the exact code I used to analyze Gene ST data for an
experiment performed with the MoGene-1_0-st-v1 array.
AROMA.AFFYMETRIX
library(aroma.affymetrix)
cdf -
On 04/12/2008, at 7:43 AM, Henrik Bengtsson wrote:
Hi,
thanks for sharing all this.
On Tue, Dec 2, 2008 at 11:54 AM, pwhiteusa [EMAIL PROTECTED]
wrote:
Hi All,
Here is the exact code I used to analyze Gene ST data for an
experiment performed with the MoGene-1_0-st-v1 array
Hi.
On Thu, Dec 4, 2008 at 5:36 AM, Benjamin [EMAIL PROTECTED] wrote:
Hi Henrik,
I'm experiencing problems with aroma.affymetrix on a linux 64bit
system. I suppose this a memory problem although the error message
sounds strange. Here is a short discription of the problem first
followed by
Hi.
On Thu, Dec 4, 2008 at 8:24 AM, Nicolas Stransky
[EMAIL PROTECTED] wrote:
Hi Henrik,
On Dec 3, 6:57 pm, Henrik Bengtsson [EMAIL PROTECTED] wrote:
quote 20081201 20:15:30| Started: 20081125 15:01:07
20081201 20:15:30| Estimated time left: 36844.5min
20081201 20:15:30| ETA
Hi.
On Thu, Dec 4, 2008 at 11:47 AM, ronmaster [EMAIL PROTECTED] wrote:
Hello,
I would like to do a Copy-number-variation analysis between tumoral
SNP chips and a common reference file. This refecence file has been
created with the apt-copynumber-workflow program from 90 hapmap chips
The updated affxparser is now available on BioC. Let me know if this
solves your latest problem. /Henrik
On Fri, Dec 5, 2008 at 2:36 AM, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi again,
I take that patch back - it won't help you. Instead I went to the
source and fixed affxparser. I've
Hi.
On Tue, Dec 9, 2008 at 2:07 PM, Qicheng Ma [EMAIL PROTECTED] wrote:
Hi Henrik,
3) For each location, the raw CN is calculated as the chip effect
relative
to the chip effect of a normal reference sample. If no reference sample
is
available, a robust average across all samples can
Hi,
I'm pleased to announce that the CRMA v2 vignette is now available online:
Vignette 'Estimation of total copy numbers using the CRMA v2 method (10K-6.0)'
http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method
The CRMA v2 method is
Hi,
this has nothing to do with the new CDF nor the Windows Shortcut
links, but instead a Windows specific limit of the length of the
absolute path/pathname you are trying to create. Yours are too long.
Your current directory is:
rootPath - C:/Documents and Settings/Elizabeth/My
Hi.
On Sun, Dec 14, 2008 at 7:46 PM, Christina christina.cur...@gmail.com wrote:
Hi Henrik,
I noticed that AromaCellSequenceFile has been updated. What is the
best way to use this to map sequence information back to the all
indices (or units, trickier I realize)? I can access the sequence
Hi,
thanks for reporting this. Could someone out there, please build OSX
universal binaries of matrixStats on *R v2.8.x*? You can get the
source of latest version by:
source(http://www.braju.com/R/hbLite.R;);
hbGet(matrixStats, 0.1.3, tar.gz);
For more details, see on how to build a
);
/Henrik
On Sun, Dec 14, 2008 at 5:39 AM, Elizabeth Purdom epur...@gmail.com wrote:
Thanks Henrik, that was the problem. My earlier version (that worked)
was 25 characters shorter than the one that failed that I emailed about.
Is that helpful?
Best,
Elizabeth
Henrik Bengtsson wrote:
Hi
Hi.
On Fri, Dec 19, 2008 at 4:35 PM, ronmaster rene.para...@gmail.com wrote:
Hi Henrik,
My colleague approach me with this brillant question relating
normalization on tumor samples. We can read
in an Affymetrix note (Genotyping console manual p173):
Probe-level Normalization for
Hi.
On Mon, Dec 15, 2008 at 10:59 PM, s...@rcega daescarc...@gmail.com wrote:
Hi Henrik!
I just analyzed 27 tumor for the 100k chip and I read the Glad paper.
I wonder the following:
Is it necessary to configure the GLAD model for the 100k Affymetrix
chip?
Not for practically purposes,
.
Cheers,
Mark
On 15/12/2008, at 9:48 AM, Henrik Bengtsson wrote:
Hi,
thanks for reporting this. Could someone out there, please build
OSX
universal binaries of matrixStats on *R v2.8.x*? You can get the
source of latest version by:
source(http
Hi,
I get a lot of request (online and offline) on sharing the CRMA v2
manuscript. The manuscript was submitted on Nov 4 to Bioinformatics
and we are still waiting to hear back from the journal and the
reviewers. When we hear back from them and if the comments are
positive, we will consider
A follow on your feedback on EBImage: It great that you share this
here. I suggest though that you also report this to the maintainer of
EBImage and possibly also to the Bioconductor list, because there you
will reach more users of EBImage, and hopefully also some useful
suggestions.
Cheers
is now build for R v2.8.x.
/Henrik
On Mon, Dec 29, 2008 at 9:23 PM, Lynn Amon la...@fhcrc.org wrote:
Hey, that does work!!
Thanks!
Lynn
Henrik Bengtsson wrote:
Hi,
for matrixStats, try to force the following installation in a fresh R
session:
source(http://www.braju.com/R/hbLite.R
Hi.
On Fri, Jan 9, 2009 at 6:22 PM, Pierre Neuvial pie...@stat.berkeley.edu wrote:
Hi,
I would like to perform allelic crosstalk calibration using the 3
central nucleotides instead of 1, which is the default in CRMAv2. I've
tried this:
acc - AllelicCrosstalkCalibration(csR, model=CRMAv2,
Hi,
I'm pleased to announce that we are now leaving the community of
v0.x.x projects - aroma.affymetrix v1.0.0 has been release (details at
the end). It is 3 years (and 2 days) to date since the project was
started. Since then a lot of new methods and features have been added
and more families
Hi Christian,
I'm quite swamped but I've added links the scripts that I used to
generate the existing NetAffx 26 (na26) UFL and UGP to each of the
different SNP CN chip type pages, e.g.
http://groups.google.com/group/aroma-affymetrix/web/mapping250k-nsp-mapping250k-sty
More comments below.
Hi.
On Wed, Jan 14, 2009 at 7:02 AM, connys cornelia.sche...@googlemail.com wrote:
HI,
I have read the documentation of this tool, but could not find
anything regarding the hardware requirements (computational need). I
want to analyze about 1000 samples affy 6.0 and I would also be
Hi,
could you please forward your UGP file to me; I think I know what the
problem is, but I guess it easier for me to check it myself first.
BTW, although this looks like a custom CDF - if you want to, I can put
up a group page specific to this chip type, documenting the chip type
(and either
Hi.
On Mon, Feb 2, 2009 at 1:32 PM, qichengm qicheng...@gmail.com wrote:
Hi,
Thanks for your reply.
I have 12 samples in total. If cesN contains all 12 samples:
cesNN - extract(cesN, 1:4)
cesNT - extract(cesN, 5:12)
Could I run GladModel as follows ?
glad -
Hi Michal,
it shouldn't be tedious at all - did you follow the instructions?
source(http://www.braju.com/R/hbLite.R;)
hbInstall(aroma.affymetrix)
URL: http://groups.google.com/group/aroma-affymetrix/web/download-install
That should install R.huge v0.1.6 as well, but if it for some reason
Hi,
the factor of two has to do with the number of parameters
estimated/stored, i.e. storing theta, vs (thetaA, thetaB). I cannot
reproduce this, but I one guess is that you have tried both
combineAlleles=TRUE and combineAlleles=FALSE and somehow there exist
cached indices that are reused from
Hi,
especially those zoom levels generate very large PNGs. They might be
too large for your PNG device driver. Depending on your system, there
are few different PNG drivers available to R. You can override the
one that aroma.affymetrix uses, but overriding the findPngDevice()
function.
Hi,
there are no methods of such analysis available in aroma.affymetrix,
and there is no time line for implementing that. It is of course on
our wishlist, though. Note also that LOH analysis is rather
unspecific; there are many different ways to infer LOH, of which some
depend on what kind of
Some comments:
1. The problem occurs in the internal method getUnitGroupCellMap().
This is only called once per chip type, regardless if you restart R or
not. The result is memoized (=cached to file) and reused in the
future. Thus, if you can get it to work once, you won't have the
problem
Hi.
On Tue, Feb 3, 2009 at 10:39 PM, David Rosenberg
david.m.rosenb...@gmail.com wrote:
Thank you greatly for your help. A couple of additional questions:
1.) With the affxparser writeCdfx functions, it looks as though
you are directly writing the binary data of correct endianness
. This project has achieved a bit higher priority from related
work on resequencing arrays. We are also testing out more generic
weighted estimators taking prior estimates. ...one day.
/Henrik
Thanks again.
On Feb 3, 2009, at 3:23 PM, Henrik Bengtsson wrote:
Ok, sorry I didn't answer you
Update,
I've updated affxparser so these warnings are no longer generated.
When affxparser v1.15.4 becomes available on BioC devel, you can
install it and these warnings will also go away.
/Henrik
On Tue, Feb 10, 2009 at 8:08 PM, Henrik Bengtsson h...@stat.berkeley.edu
wrote:
Hi,
first
Hi,
there's a growing list of unanswered messages on the mailing list.
FYI, right now I have no time to reply to those myself - there is a
slight chance I will be able to do it next week, but not sure. If
anyone else can help out, please try to do so. Thanks Pierre for your
answers.
/Henrik
Fixed. /Henrik
On Mon, Feb 23, 2009 at 6:24 AM, cstratowa
christian.strat...@vie.boehringer-ingelheim.com wrote:
Dear Henrik
On your web-page the link to:
Mapping50K_Xba240,na26,HB20080916.ufl
is broken
Best regards
Christian
--~--~-~--~~~---~--~~
Hi,
super busy with huge backlog so I cannot really start replying to
aroma.affymetrix questions until late next week, but I'll make an
exception for this case.
On Thu, Mar 5, 2009 at 10:41 AM, wukong wukongsu...@gmail.com wrote:
Dear aroma.affymetrix group users:
Our server suddenly went
Hi,
On Thu, Apr 9, 2009 at 1:06 PM, Matt matt.kowg...@gmail.com wrote:
Hendrik,
I was hoping you could guide through the process of using GladModel
with a sample of simulated data of raw copy number estimates for a
single chromosome. How do I create the CnChipEffectSet with just a
vector
This was due to an redesign of the EBImage data structure. This is
fixed in the latest aroma.affymetrix which supports both the old and
the new EBImage style. From the NEWS:
Package: aroma.core
===
Version: 1.1.0 [2009-05-29]
[snip]
o BUG FIX: Our internal interleave() for
library(aroma.affymetrix)
for loading the package.
/H
On Thu, Jun 4, 2009 at 8:45 AM, Myriam Peyrard myriam.peyr...@ki.se wrote:
Ok, thank you so much, Pierre. I shall try and if not working, get back
to you again.
The output I gave you was the one I got but, finally (my second day
using
Hi.
On Mon, Jun 8, 2009 at 1:53 PM, marcomazu.c...@gmail.com wrote:
Dear Henrik,
I have 2 samples hzbridiyed on SNP6 in respctively 5 and 6
replicates. I would like to pool them ann estimate the relative CNVs.
Is this fragment of code doing that? Or you have any other
suggestions?
cdf
On Mon, Jun 8, 2009 at 8:18 PM, chunjiang hecamel...@gmail.com wrote:
Hi,
Thanks.
I also have some questions when I use the apt-cel-transformer tool.
Does the command like this:
apt-cel-transformer.exe --clf-file MoEx-1_0-st-v1.r2.clf -c rma.bg... -o
output *.cel
I cannot run through it
Has nothing to do with data quality here. Search the group for
Cannot fit normalization function to enzyme and you'll find the
answer in the first match; you forgot to fit the PLM.
/Henrik
On Tue, Jun 9, 2009 at 7:17 AM, marcomazu.c...@gmail.com wrote:
Dear Henrik,
I have installed the
Hi,
from the message
install.packages(pkgs = aws, type = source, lib =
/home/cathy/R/i486-pc-linux-gnu-library/2.6...
it looks like you have some really old settings hanging around, e.g.
R_LIBS. What does
print(.libPaths())
report?
Check Sys.getenv(R_LIBS), it might be set in your
Hi,
update aroma.affymetrix et al. and retry.
/Henrik
On Thu, Jun 18, 2009 at 5:01 AM,
cstratowachristian.strat...@vie.boehringer-ingelheim.com wrote:
Dear all,
Below I show you the relevant code fragments of my function computeCN
() to compute copy-number regions using model CBS. This
Hi.
2009/6/24 marco mazu.c...@gmail.com:
Dear Henrik,
I wonder if aroma.affymetrix is suitable for pooled GWA studies and
if you have any experience with this subject. In principle this
consists in extracting the RAS scores, so should be doable. I have the
following specific questions
-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: den 18 juni 2009 18:25
To: aroma-affymetrix@googlegroups.com
Subject: Re: No CN estimates for SNP 6.0 (Was: Re: [aroma.affymetrix] Re:
CNV analys 28 st SNP 6.0 arrays)
Hi,
are you saying you do not get results from any
to work. However, I
only support and run redundancy tests on the lastest stable version of
R (now R 2.9.x).
Did you try?
/Henrik
Best regards
Christian
On Jun 18, 5:39 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi,
update aroma.affymetrix et al. and retry.
/Henrik
On Thu, Jun
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: den 29 juni 2009 01:12
To: aroma-affymetrix@googlegroups.com
Subject: [aroma.affymetrix] Re: No plot CNV analysis (Myriam)
Hi,
my initial guess is that the when the fragmentation-length
normalization failed
that is
specified. It does not mean it is guaranteed to work. However, I
only support and run redundancy tests on the lastest stable version of
R (now R 2.9.x).
Did you try?
/Henrik
Best regards
Christian
On Jun 18, 5:39 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi,
update
@googlegroups.com
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: den 29 juni 2009 10:03
To: aroma-affymetrix@googlegroups.com
Subject: [aroma.affymetrix] Re: No plot CNV analysis (Myriam)
In directory
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs
Hi,
all constructor functions defined via setConstructorS3() get class
'Class' and all such Class functions must accept a call without
arguments. That is, you must design Sample() such that you can call
it as
obj - Sample()
You can differentiate between NULL and say numeric(0).
The reason
Hi,
it was not clear from your first message that you wanted to move CEL
files (there are many Affymetrix files that have a chip type).
The most low-level way to query a CEL file for its chip type is
provided by the affxparser package:
library(affxparser);
pathnames - list.files(path=dataPath,
R.cache_0.1.7
R.utils_1.1.6
[19] R.oo_1.4.6 R.methodsS3_1.0.3
Best regards
Christian
On Jun 29, 4:34 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi.
On Mon, Jun 29, 2009 at 5:14 AM,
cstratowachristian.strat...@vie.boehringer-ingelheim.com wrote:
Dear
Hi,
thanks. I've attached a script illustrating how to allocate an empty
Aroma Cell Sequence (*.acs) file and then import probe sequences from
an Affymetrix probe tab file. Hopefully that show to do it.
If you build UGP, UFL, ACS or other files, please consider sharing it
here. As soon as we
a bit of experience
setting up sites using django.
On Jun 29, 2009, at 3:07 PM, Henrik Bengtsson wrote:
Hi,
has any of you experience with Joomla, Drupal or other content
management systems (CMSs)? We wish/need to migrate the documentation
from the current aroma.affymetrix Google Group
Hi.
On Tue, Jul 21, 2009 at 9:23 PM, Stellaw Chaostellaw.c...@gmail.com wrote:
Dear aroma.affymetrix developers,
I am a little bit confused while using ur package aroma.affymetrix to
process my dataset.
The following is my code——
setwd(C:/Array Files_CP2Bonly)
library(aroma.affymetrix)
To add to the list of references, see also:
Yamamoto, G.; Nannya, Y.; Kato, M.; Sanada, M.; Levine, R. L.;
Kawamata, N.; Hangaishi, A.; Kurokawa, M.; Chiba, S.; Gilliland, D.
G.; Koeffler, H. P. Ogawa, S. Highly sensitive method for genomewide
detection of allelic composition in nonpaired,
plots that might be interesting for other users.
You can attach PNGs to email messages posted to the mailing list, but
you cannot do this via the web interface.
/Henrik
Best Regards
Marco
On 26 Juni, 07:35, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi.
2009/6/24 marco mazu.c
of small to very large Affymetrix
data sets(which is written by you in August, 2007 =D).
It took me a while to figure out which you one meant; it's the slides
used in my BioC2007 lab:
Henrik Bengtsson, aroma.affymetrix - Analysis of small to very large
Affymetrix data sets, Bioconductor Workshop
be
outdated. Restriction enzyme fragmentation and fragment lengths etc
only applied do DNA/SNP analysis and does not make sense for gene
expression analysis.
Cheers,
Henrik
Thank you,
Anqi
On Jul 22, 5:09 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi.
On Tue, Jul 21, 2009
Hi.
2009/7/23 ZZ zhu0...@gmail.com:
Hi,
I'm trying to do some copy number analysis of SNP6 data with
aroma.affymetrix package. I followed the instructions for cRMA v2
(followed by CBS segmentation). The codes ran smoothly except for the
occasional appearance of the following message:
Hi,
the aroma.affymetrix annotation files have an na-tag indication the
NetAffx release/version, e.g.
Mapping250K_Nsp,na26,HB20080915.ugp
From this we know that data from the Affymetrix NetAffx release 26 was
used. From there you have to go to the NetAffx Analysis Center to
find out what
Thanks Mark,
sorry I wasn't clear. The hbLite() command will not install missing
CRAN/BioC packages, which is why you would expect an error if you
remove required CRAN packages such as digest. Those hbLite() commands
were only intended for troubleshooting Michael's setup.
Michael, also, after
2009/8/19 ssv ssv@gmail.com:
Hi Henrik
[snip]
An unrelated question: Is cbsmodel is the same as that (cbs)
implemented in DNAcopy ? From the loaded packages, I can see DNAcopy
package. When i ran DNAcopy independently (by supplying values
externally in a tsv), on the same samples that
Hi.
On Mon, Aug 24, 2009 at 12:21 PM, mbaudismbau...@gmail.com wrote:
Dear all,
I have posted a script and associated files to make it easier to:
1. process various types of Affymetrix genotyping array batches, using
aroma.affymetrix, but with
2. (IMHO) improved value segmentation
Did you see my reply to your previous message on this?
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/0a820ee786a219e5
/Henrik
On Thu, Aug 27, 2009 at 7:34 AM, gunes gundemguguni...@gmail.com wrote:
Hi,
I am running a paired analysis for 2 tumor samples following
- Discussion' started on Aug 27, 2007 [
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/9ee424979095c462
].
Cheers,
/Henrik
Thanks in advance,
Diya
On Aug 27, 12:39 am, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi.
On Wed, Aug 26, 2009 at 12:10 PM, Diya
files).
/Henrik
By
Sukhbir Singh Rattan.
On Thu, Aug 27, 2009 at 11:15 AM, Henrik Bengtsson h...@stat.berkeley.edu
wrote:
On Wed, Aug 26, 2009 at 10:29 PM, Sukhbir
Rattansukhbir.rat...@gmail.com wrote:
Hi Everyone,
I have 15 Affymetrix CEL files represent three pH conditions
Hi.
On Thu, Aug 27, 2009 at 12:10 PM, yupuyupuli...@gmail.com wrote:
Hi,
I am trying to run gcrma background correction on 10 SNP6.0 data. I
download the probe_tab files from affymetrix:
GenomeWideSNP_6.CN_probe_tab and GenomeWideSNP_6.probe_tab
and I got the following error of my first
Hi,
see Vignette 'Estimation of total copy numbers using the CRMA v2
method (10K-6.0)' under
http://groups.google.com/group/aroma-affymetrix/web
/Henrik
PS. It helps us to help you if you let us know where you got your script from.
On Tue, Sep 1, 2009 at 2:55 AM, sachinkrsac...@gmail.com
On Mon, Aug 31, 2009 at 11:42 PM, ssvssv@gmail.com wrote:
Hi Henrik
Here are the links:
1)
http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0
Under Identification of copy-number regions
cbs - CbsModel(ces1, ces2)
From the vignette and section your
On Tue, Sep 1, 2009 at 7:53 AM, Henrik
Bengtssonhenrik.bengts...@gmail.com wrote:
On Mon, Aug 31, 2009 at 11:42 PM, ssvssv@gmail.com wrote:
Hi Henrik
Here are the links:
1)
http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0
Under Identification of
No worries at all - I just want you and everyone else to know how to
make this forum more effective, which is somewhat explained in that
FAQ. 2008-03-26:
http://groups.google.com/group/aroma-affymetrix/web/frequently-asked-questions
Cheers,
Henrik
On Tue, Sep 1, 2009 at 11:58 AM,
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