Hi there,
thanks all for citing our publication directly or indirectly related
to the aroma project framework.
Since I noticed that the original CRMA paper often get cited even when
the CRMA v2 method is used/meant, I would like to clarify to the list
that CRMA v2 is preferably referenced as:
that min.width=5 worked only in the first sample. Do
you have any idea on this? Thanks!
Best,
Kai
On Oct 26, 9:09 pm, Henrik Bengtsson henrik.bengts...@aroma-
project.org wrote:
I forgot to say that in the next release of aroma.core package, you
will be able to specify additional arguments when
help. I look forward to hearing from you soon.
Best,
Kai
On Sep 27, 9:47 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi.
On Mon, Sep 27, 2010 at 4:51 PM, Kai wangz...@gmail.com wrote:
Hi Henrik,
I was wondering whether there is a way I can fine tune the behavior
Hi.
On Wed, Oct 13, 2010 at 5:24 PM, Yue Hu yuehu.m...@gmail.com wrote:
Hi,
Just shift from affymetrix to agilent recently and since I prefer
the plot generated by aroma.affymetrix I am just wondering if
aroma.affymetrix is able to handle agilent chip data in some way.
When you say plot
Hi.
On Thu, Oct 14, 2010 at 4:38 AM, allab asphod...@googlemail.com wrote:
Dear aroma users/authors,
i am doing now Affy 6.0 SNP data analysis and my goal is to become BAF
values so that i can further use them with the method SOMATICS
(Assie'08).
I have not used from the very beginning the
Thanks for follow up/reporting back to the list.
/Henrik
On Thu, Oct 14, 2010 at 12:03 PM, Fong fongchunc...@gmail.com wrote:
For those interested I got a reply from the makers of the CDF files
and apparently it is an issue on their end. Here is their reply:
We have been studying the
, 2010 at 1:47 AM, Henrik Bengtsson h...@aroma-project.org
wrote:
Hi,
sorry, my mistake. I missed that you already did this.
You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
You can download it from Affymetrix and you'll find a link to their
support page via http
Hi.
On Wed, Sep 29, 2010 at 8:00 PM, Dario Strbenac
d.strbe...@garvan.org.au wrote:
Hello,
I remember reading a while ago that you can pass in additional parameters to
CbsModel, and they will get passed onto DNAcopy functions. However, it
doesn't seem to be working for me. I don't want any
file conversion and so on. That's why it
is crucial to know more about the chip used.
I also recommend that you try dChip and/or Affymetrix GTC, if possible.
/Henrik
Thanks,
Patrick
On Sun, Sep 26, 2010 at 1:36 PM, Henrik Bengtsson h...@aroma-project.org
wrote:
Hi.
On Mon, Sep 13, 2010
also recommend that you try dChip and/or Affymetrix GTC, if possible.
Since it is GenomeWideSNP_6, you should be able to try it on Affymetrix GTC.
/Henrik
/Henrik
Thanks,
Patrick
On Sun, Sep 26, 2010 at 1:36 PM, Henrik Bengtsson h...@aroma-project.org
wrote:
Hi.
On Mon, Sep 13, 2010
Hi.
On Mon, Sep 27, 2010 at 4:51 PM, Kai wangz...@gmail.com wrote:
Hi Henrik,
I was wondering whether there is a way I can fine tune the behavior of
CbsModel. Sometimes the default algorithm produces too many small
fragments right next to each other without much separation in mean
copy
, Henrik Bengtsson h...@aroma-project.org
wrote:
Hi,
first of all, for this chip type you need to specify:
bc - GcRmaBackgroundCorrection(csR, type=affinities);
Moreover, you cannot use the custom CDF in the
GcRmaBackgroundCorrection step, and have to do the follow workaround
illustrated
Hi,
On Fri, Sep 24, 2010 at 1:27 PM, Vonn vwal...@email.unc.edu wrote:
Hi All,
I'm using aroma to analyze CEL files from 141 SNP 6.0 arrays. I fit
the quality assessment model as follows:
plm = RmaPlm(csR)
fit(plm, verbose = log)
qam = QualityAssessmentModel(plm)
Then I'd like to
Hi,
first of all, for this chip type you need to specify:
bc - GcRmaBackgroundCorrection(csR, type=affinities);
Moreover, you cannot use the custom CDF in the
GcRmaBackgroundCorrection step, and have to do the follow workaround
illustrated in the below example:
library(aroma.affymetrix);
Hi.
On Mon, Sep 13, 2010 at 4:19 PM, Patrick patrickjdana...@gmail.com wrote:
Hi everyone,
I'm using AROMA's implementation of the CRMA v2 method to get copy
number estimates for cancer samples, and I'm getting a very unusual
result. Many of the samples have a chromosome where AROMA has
for alternatives that are accessible
from within China, and the above seem not to be. It would be great to
solve this, because the archive is very useful resource.
Thanks
Henrik
On Tue, Sep 21, 2010 at 9:32 PM, Henrik Bengtsson h...@aroma-project.org
wrote:
Hi,
it has been brought to my attention
this helps
/Henrik
Best,
Kai
On Sep 20, 1:06 pm, Henrik Bengtsson h...@aroma-project.org wrote:
Hi Kai.
I am aware of the issue, and it is on the todo list to add argument
specify that you don't want ratios to be calculated. There is
currently a secret workaround for this that should
Hi Dario,
Pierre Neuvial has kindly provided a more up-to-date vignette for
doing paired total copy number analysis. You find it at:
http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis
See if that helps
/Henrik
On Wed, Sep 22, 2010 at 5:05 PM, Dario Strbenac
Hi Kai.
I am aware of the issue, and it is on the todo list to add argument
specify that you don't want ratios to be calculated. There is
currently a secret workaround for this that should not be read as an
official documented feature [that's a warning for users reading this
thread in the
Hi.
On Fri, Sep 17, 2010 at 12:58 PM, Matt matt.kowg...@gmail.com wrote:
Hi Henrik,
I am processing the data from the 270 HapMap samples on the SNP 6.0
arrays using the CRMAv2 method. I wrote a script to follow the steps,
minus the plotting, outlined on
Hi,
On Tue, Aug 24, 2010 at 3:01 AM, Denis amer.ak...@rub.de wrote:
Hi Henrik,
Sorry for the delay, I had some difficulties in getting GLAD strated
(including gsl ...).
What should I else say than your the best and thank you very much for
your help. I finally got it. I would like to
Hi,
if you are following Pierre's advice and still getting *that* error
message my best guess is that you are getting an error while
installing one of the packages that aroma.affymetrix depends on, which
in turn probably will fail the installation of aroma.affymetrix
itself. The reason why one
Hi Denis,
you refer to the thread 'Custom Canine SNP' started on July 18, 2008.
In KD's message on August 14, 2008 you can see how he explicitly set
argument genome=Canine when he sets up the GLAD model. From the
verbose output I can see you are using CBS, but it is not clear how
you set it up.
important it
is to not overlook the smallest details in scientific communication
since they can make big differences.
Cheers,
Henrik
Thank you for your help.
Best regards
Christian
On Aug 2, 2:54 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi.
On Mon, Jul 26, 2010 at 12:00 PM
() on
the same array set at the same time.
/Henrik
I hope that this explanation could explain better what the different
steps are.
Best regards
Christian
On Jul 23, 4:35 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi.
On Jul 22, 10:24 am, cstratowa christian.strat
Hi Steven.
On Mon, Jul 26, 2010 at 9:00 PM, Steven Bosinger
steven.bosin...@gmail.com wrote:
Hi,
I'm new to aroma and bioC in general, so these are probably a very
straightforward questions:
I am using aroma to get QC on some Human Affymetrix Gene arrays.
1. To keep it consistent with
Hi Fong(?).
On Sat, Jul 24, 2010 at 2:10 AM, Fong fongchunc...@gmail.com wrote:
Hi,
I've used aroma.affymetrix to generate and extract the probeset
summaries (chip effects) from a set of Human Exon array samples I
have. And then performed batch adjustment on these probeset summaries
using
Hi Sundar,
I've been leaving your messages to the FIRMA experts, because they can
better answer you questions. However, I'll give a quick reply to the
things I can answer.
On Mon, Aug 2, 2010 at 6:59 PM, Sundar sundar...@gmail.com wrote:
Hi,
I am trying to analyze Mouse Exon 1.0 st
Hi,
I'll leave the details to FIRMA experts, but you are using really
large values of argument 'ram'. It might be that you ran out of
memory (the you got an error message). If you used cut'n'paste,
instead of source(), to do the analysis, it might be that one of the
fit() methods was
Hi all,
new versions of aroma.affymetrix and friends have been released. It
is highly recommended to update:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
In addition to some added features, there were also a few bugs fixed
in this release. Thanks for the reports!
Hi,
it's hard to say what causing this, but if you see it in several
samples at the same location, then my immediate thought is that you
reference signal may carry it. Are you using the average of the pool
of all samples as a reference or how do you calculate it? How many
samples to you have
opinion?
You suggestion makes sense for dataset specific temporary files etc,
but again, I don't think that is the case here. Instead I think we
are misunderstanding each other. You script will help.
/Henrik
Best regards
Christian
On Jul 21, 6:46 pm, Henrik Bengtsson henrik.bengts
?
Your suggestion makes sense for dataset specific temporary files etc,
but again, I don't think that is the case here. Instead I think we
are misunderstanding each other. You script will help.
/Henrik
Best regards
Christian
On Jul 21, 6:46 pm, Henrik Bengtsson henrik.bengts...@gmail.com
[sorry my repost did not contain my full reply due to a cut'n'paste
error.]
Hi Nicolas.
On Tue, Jul 20, 2010 at 11:42 AM, Nicolas Vergne
nicolas.vergne@gmail.com wrote:
Hi everybody,
I use ACNE for the normalization of SNP6.0 chip arrays.
As ACNE is a multi-array methode, I would like to
to delete any .Rcache/ as long as no R session
is in the process of writing to it. It's a cache containing redundant
information.
Best regards
Christian
On Jul 2, 12:47 am, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi Christian.
On Tue, Jun 29, 2010 at 3:39 PM, cstratowa
to delete any .Rcache/ as long as no R session
is in the process of writing to it. It's a cache containing redundant
information.
Best regards
Christian
On Jul 2, 12:47 am, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi Christian.
On Tue, Jun 29, 2010 at 3:39 PM, cstratowa
[reposting; the forum has hiccups and does not put my replies in the
archives or deliver to everyone.]
Hi Nicolas,
thanks for reporting this unwanted feature. I've fixed it so that the
default filename is *,total.txt and *,fracB.txt, respectively. Until
the next release is available, you can
Hi, please ignore this message. I am trying to figure out why messages
that I have sent (group owner) yesterday have not been delivered to
the group and mailinglist archive. /Henrik
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to
Hi Markus,
sorry but this one slipped through my net.
On Thu, Jun 17, 2010 at 5:27 PM, Smaug72 leber.mar...@gmx.de wrote:
Dear Henrik,
unfortunately we are faced with another problem.
We processed several CEL files with CRMAv2 as decribed by vignette:
Hi,
before continuing, do you have the latest version of aroma.affymetrix
(v1.6.0) installed, e.g. what does
library(aroma.affymetrix);
print(sessionInfo());
report? You probably also want to update to R v2.11.1 (R v2.9.0 is rather old).
Second, the annoationData/ directory should be located
Hi Richard,
sorry for the delay - this one slipped through and I simply missed our
message, but I caught it while troubleshooting the same problem
reported in thread 'ArrayExplorer issue' started on 2010-07-02.
The reason for your problems is a bug in aroma.core/R.filesets that
causes hiccups
Hi Johan,
On Wed, Jun 30, 2010 at 9:13 AM, Johan Staaf johan.st...@med.lu.se wrote:
Dear Henrik,
I get an error when trying to extract CRMAv2 processed data when using the
extract() function like below.
cesSamples - extract(cesNList[[chipType]], assay.vector)
The error occurs when the
It sounds like on of your CEL files are corrupt. Start out with the 5
CEL files that work and add other CEL files one by one to the
directory to figure out which work and which do not. Also, the CEL
files should roughly be of the same file size; if one is much
different that is a likely clue
Please see FAQ. 2007-05-24 on http://aroma-project.org/FAQ
/Henrik
On Fri, Jun 25, 2010 at 10:49 AM, Liang Cheng vikingch...@gmail.com wrote:
Henrik,
I found that if I want to read CEL files, I have to get the CDF files. Where
can I get the ones mentioned in your slider, especially the 250k
Hi Christian.
On Tue, Jun 29, 2010 at 3:39 PM, cstratowa
christian.strat...@vie.boehringer-ingelheim.com wrote:
Dear Henrik,
Until now I have used aroma.affymetrix_1.1.0 with R-2.8.1 and could
run my analysis on our sge-cluster w/o any problems.
Now I have upgraded to R-2.11.1 and to
Hi Johan,
this certainly looks like a computational hiccup. I never seen it,
though I can imagine various ways how it could happen. Instead of
guessing, do you have a complete script that you did, you did you type
the commands on the command line one by one? You are saying you did
the analysis
Hi.
On Wed, Jun 23, 2010 at 11:04 AM, mortiz mortiz...@gmail.com wrote:
hi everyone,
im trying to develop a function based on FragmentLengthNormalization,
but when i try to execute my new function it gives me the next error
message:
Error in process.NormalRegions(normalReg, verbose =
Hi Mamum,
On Fri, Jun 18, 2010 at 12:25 PM, Mamun Rashid mamunbabu2...@gmail.com wrote:
Hi everyone,
I am analysing some affymetrix exon array data. I have been performing some
Quality checking of the data. I have plotted the residulas from the plm fit
of
raw intensity data.
I am using
you
2010/6/23 Henrik Bengtsson h...@stat.berkeley.edu
On Wed, Jun 23, 2010 at 7:00 AM, Liang Cheng vikingch...@gmail.com
wrote:
Thank you, Henrik
So there is no function from aroma package, which can deal with the
xx.cel
file?
Please explain what you mean deal
Hi.
On Mon, Jun 21, 2010 at 2:26 PM, Albyn albyn.dhun...@gmail.com wrote:
Dear all,
I am new to R and aroma.affymetrix both. I have 25 SNP6.0 Cel files
and I have to find out LOH and UPD. I would like to use
aroma.affymetrix could anybody suggest me if it is a good idea to use
this
Hi Jack.
On Mon, Jun 7, 2010 at 3:36 PM, Jack Yu j.yu...@gmail.com wrote:
Hello,
I sent an e-mail earlier regarding errors in running the total copy
number vignette, but please disregard that as it turns out it was just
an issue with the annotation files. Sorry for the inconveniences.
Good.
the signals after ACC. It looks like the data is zoomed in
to the lower quantiles.
So, if you redo those plots after ACC with a great xlim, e.g.
xlim=5*xlim it might not look that bad after all.
/Henrik
On 5 Jun 2010, at 16:42, Henrik Bengtsson wrote:
Hi.
On Thu, Jun 3, 2010 at 4:59 PM, seth
Hi.
On Mon, Jun 7, 2010 at 4:41 PM, k o ott4...@gmail.com wrote:
Dear Usergrop.
while proccessing data from the 5000k Sty array (but not the Nsp set),
I receive the folleowing error:
acc - AllelicCrosstalkCalibration(csR, model=CRMAv2)
csC - process(acc)
Error in sort.list(pairsToBuild) :
/Henrik
...
acc - AllelicCrosstalkCalibration(csR, model=CRMAv2);
csC - process(acc, verbose=-10);
plotAllelePairs(acc, array=array, pairs=1:6, what=input, xlim=1.5*xlim);
On 28 May 2010, at 17:59, Henrik Bengtsson wrote:
Hi.
On Thu, May 27, 2010 at 6:17 PM, seth redmond
seth.redm
when you did.
/Henrik
Best Regards
Robert
On Jun 2, 6:47 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi.
On Wed, Jun 2, 2010 at 11:16 AM, Ivanek, Robert robert.iva...@fmi.ch wrote:
HI Henrik,
I was a little bit investigating the error and I found out that some
also the UFL and UGP files?
Best Regards
Robert
On May 30, 7:27 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote:
Hi.
On Wed, May 26, 2010 at 3:24 PM, Ivanek, Robert robert.iva...@fmi.ch
wrote:
Dear Sir or Madam,
I would like to analyse the copy number variation data from
Hi.
On Wed, May 26, 2010 at 3:24 PM, Ivanek, Robert robert.iva...@fmi.ch wrote:
Dear Sir or Madam,
I would like to analyse the copy number variation data from Affymetrix
Mouse Diversity Array. I have not found any information on your website
about this particular array.
I have created page
Hi.
On Tue, May 18, 2010 at 5:39 AM, Tae-Hoon Chung hoontaech...@gmail.com wrote:
Hi, All;
I have a simple question: What's the best way of performing multiple
processing jobs of the same platform (Affymetrix SNP chips)?
My concerns are as follows: (1) Many of the jobs involving Affymetrix
Hi.
On Sat, May 15, 2010 at 6:10 PM, Gabriele Zoppoli zopp...@gmail.com wrote:
Hi,
I'm new here, and I'm sorry if I'll post obvious questions. I looked
throughout the newsgroup and on the aroma.affymetrix web page, but I
couldn't find the answer from my question, so here it is:
I'm trying
Hi all,
aroma.affymetrix and friends have been updated and is now being rolled
out to the CRAN servers. It is highly recommended to update:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
This update follows the April releases of R v2.11.0 and Bioconductor
v2.6, which
Hi.
On Fri, May 14, 2010 at 10:36 AM, Markus Leber leber.mar...@gmx.de wrote:
Dear Henrik,
thank you very much for your support.
You are right. I am sorry that I didn't notice this problem.
Step Calibration for crosstalk between allele probe pairs works without
problems now.
Hi.
On Wed, May 12, 2010 at 12:23 PM, Smaug72 leber.mar...@gmx.de wrote:
Dear Henrik,
thank you very much for your reply.
Again I installed R and CRMA v2 on a new virtual machine (Suse 11.2),
so that I can step back if necessary.
To get the terms correct; you installed the aroma.affymetrix
has 'Encoding' field and re-encoding is not possible
TH
2010/5/10 Henrik Bengtsson h...@stat.berkeley.edu
Ok.
This could be an issue with affxparser and 64-bit OSX; recent problem
reports with affxparser has been with 64-bit OSX.
You are running R v2.10.x, which is outdated. The new
Hi.
On Tue, May 11, 2010 at 2:42 PM, Smaug72 leber.mar...@gmx.de wrote:
Dear Henrik Bengtsson,
we would like to use the CRMA v2 for our work.
Unfortunately we receive errors.
First we use a Linux system (Suse 11.2).
I installed R (version 2.11.0) without any problems.
Afterwards I
What does
print(sessionInfo());
report after doing library(aroma.affymetrix)?
/Henrik
On Mon, May 10, 2010 at 4:47 AM, Chung Tae-Hoon hoontaech...@gmail.com wrote:
Hi, All;
I was trying to process Affymetrix 250K Sty SNP Chip of HapMap project using
CRMAv2 algorithm.
I was following
] R.filesets_0.8.0 digest_0.4.2 R.utils_1.4.0
[13] R.oo_1.7.1 R.methodsS3_1.2.0
I am using 64-bit R-2.10.1 on Mac OS x.
TH
-Original Message-
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Hi,
before doing anything else, please provide what
print(sessionInfo())
reports.
/Henrik
On Wed, Apr 28, 2010 at 12:43 PM, Nolwenn Le Meur nlem...@gmail.com wrote:
Hi everyone,
I am trying to analyze pooling-based GWAS (I am used to expression
data but new to the GWAS field) .
I have 2
Hi.
On Thu, Apr 22, 2010 at 9:26 PM, mike dewar mikede...@gmail.com wrote:
Hi,
I'm trying to normalize data generated by the immunological genome
project (immgen.org). They have released raw data for 128 arrays and I
would like to preprocess their data. I'm very new to this, so
apologies
: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Thursday, April 22, 2010 7:46 PM
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] failure of AllelicCrosstalkCalibration on
R-2.11
Hi.
On Thu, Apr 22, 2010 at 11:13 PM, Karl
@googlegroups.com
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Friday, April 23, 2010 6:02 AM
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] failure of AllelicCrosstalkCalibration on
R-2.11
On Fri, Apr 23, 2010 at 2:20 AM, Karl Kornacker
kornac
Hi.
On Thu, Apr 22, 2010 at 11:13 PM, Karl Kornacker
kornac...@midohio.twcbc.com wrote:
The key function AllelicCrosstalkCalibration has stealth dependencies on
additional packages (sfit and/or expectile) which are currently unavailable
for R-2.11. When might updated versions of these packages
Please report your sessionInfo(). /Henrik
On Wed, Apr 21, 2010 at 11:51 AM, elodie elodie.chapeaubl...@gmail.com wrote:
Hi,
I try to use aroma.affymetrix for Human Exon chip with custom CDF. I
tested several BrainArray custom CDF (refseq, ense, vegae). Before, I
used convertCdf() to convert
Hi.
On Tue, Apr 20, 2010 at 10:16 AM, mortiz mortiz...@gmail.com wrote:
hi everyone,
I need to read the sequences of the probes from the GWS6.0 chip and it
has taken me more than 12 hours to do it only for 2 chromosomes. Im
guessing im doing something wrong, because the
Hi.
On Thu, Apr 15, 2010 at 10:56 AM, step...@mnemosyne.co.uk
step...@mnemosyne.co.uk wrote:
Dear aroma users,
I am trying to run gcrma across a collection of human breast cell line CEL
files without success - code has worked in previous aroma versions, and is
still contemporary with
= cdf, ...)
at withCallingHandlers(expr, warning = function(w)
invokeRestart(muffleWarnin
at su
R
R bc - GcRmaBackgroundCorrection (cs)
R csB - process (bc, verbose = -10) # as suggested by Henrik
Bengtsson
Background correcting data set...
Error in file(con, rb) : cannot open
-
v1,fullR1,A20080718,MR) # taken from http://www.aroma-project.org/node/31
R cs - AffymetrixCelSet$byName (affy-brain-dev, cdf = cdf) #
produces cell set class object
R
R bc - GcRmaBackgroundCorrection (cs)
R csB - process (bc, verbose = -10) # as suggested by Henrik
Bengtsson
Background
Hi,
in a few moments, I will update a few pages on the aroma.affymetrix
Google Group so that they point to the new website
http://www.aroma-project.org/. This may cause the aroma.affymetrix
mailing list/forum to go down, meaning if you try to post a message a
message will bounce back to you with
Hi.
On Fri, Mar 26, 2010 at 9:17 PM, Louie van de Lagemaat
louie...@gmail.com wrote:
Hi Henrik et al,
I have been reanalyzing an older dataset of Mapping500K (Nsp+Sty)
arrays for CNVs using aroma, and this works in general really well.
However, I have noticed that overall many individuals in
very much,
Dick
On Fri, Mar 26, 2010 at 2:18 AM, Henrik Bengtsson
henrik.bengts...@gmail.com wrote:
Hi,
On Thu, Mar 25, 2010 at 7:20 PM, Richard Beyer rpbe...@gmail.com wrote:
Hi Henrik,
I'm quite enjoying aroma-project.org. Thanks for your detailed help.
I am making some progress now
= as.character(1:35),fill=rainbow(35))
plotDensity(cs,col=rainbow(35),ylim=c(0,0.7),types=pm)
legend(0,0.7,legend= as.character(1:35),fill=rainbow(35))
Cheers,
Dick
On Thu, Mar 25, 2010 at 10:06 AM, Henrik Bengtsson
henrik.bengts...@gmail.com wrote:
Hi.
On Thu, Mar 25, 2010 at 5:02 PM
Hi,
GCRMA is not fully supported for all chip types, and I haven't checked
if MoEx-1_0-st-v1 is one. But, first, lets fix some other mistakes
you're doing.
On Wed, Mar 24, 2010 at 4:48 PM, Gil Tomás gil@gmail.com wrote:
Dear all,
I am trying to normalize a dataset hybridized with
Hi.
On Sun, Mar 14, 2010 at 3:04 AM, Yong pkuonl...@gmail.com wrote:
Hi Everyone,
I kind of remember that it is difficult or not correct to analyze
multiple datasets based on different array design like hgu133plus2 and
HuEx-1_0-st-v2. So, I am wondering whether it is OK to pool different
.
Thanks again,
Dick
On Thu, Mar 25, 2010 at 8:26 AM, Henrik Bengtsson
henrik.bengts...@gmail.com wrote:
Hi.
On Thu, Mar 25, 2010 at 5:30 AM, dbe...@u.washington.edu
rpbe...@gmail.com wrote:
Hello,
I would like to get more info, perhaps example calls, on the various
subclasses
of aroma.affymetrix doesn't support the MoEx-1_0-
st-v1 chip? How could I infer that?
On Mar 25, 3:26 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi,
GCRMA is not fully supported for all chip types, and I haven't checked
if MoEx-1_0-st-v1 is one. But, first, lets fix some other mistakes
Hi,
I leave this one to Mark Robinson who is designed createUniqueCdf()
for AffymetrixCdfFile and is on top of this. Though, in the meanwhile
could you please:
1. Clarify the origin of Mm_PromPR_v02.CDF, because Affymetrix does
not provide an CDF.
2. Make the Mm_PromPR_v02.CDF available to us?
, ...)
at byPath(static, path = path, cdf = cdf, ...)
at withCallingHandlers(expr, warning = function(w)
invokeRestart(muffleWarnin
at suppressWarnings({
at method(static, ...)
at AffymetrixCelSet$byName(tissues, cdf = cdf)
Many thanks,
Daniela
On Mar 9, 5:12 pm, Henrik Bengtsson
thankful!
More comments below...
Many thanks,
Daniela
On Mar 9, 4:56 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi,
please let us know what your source of documentation is, e.g.
webpages, because you are using method names that are either outdated
or non-public. Then I'll answer
On Mon, Mar 1, 2010 at 6:38 PM, zaid z...@genomedx.com wrote:
Is there support for aroma.affymetrix under R 64 bit?
Definitely on Linux. Are you asking about Windows 64-bit? Then, I
think so, cf:
http://cran.r-project.org/web/checks/check_results_aroma.affymetrix.html
but I don't have
reason
affxparser seems to be unavailable.
On Mar 1, 9:48 am, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
On Mon, Mar 1, 2010 at 6:38 PM, zaid z...@genomedx.com wrote:
Is there support for aroma.affymetrix under R 64 bit?
Definitely on Linux. Are you asking about Windows 64-bit? Then, I
Hi.
On Tue, Feb 23, 2010 at 3:36 AM, Alfredo Hidalgo
ahida...@inmegen.gob.mx wrote:
Hi!
We are interested in running a GISTIC analysis on the data we obtained after
segmentation with GLAD with Aroma, but there seems to be a problem regarding
the start and end postions of the segments, which
no luck.
Thanks in advance
On Feb 24, 10:46 am, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi,
there are probably more output from the error, or ? If so, could you
please provide us with that one? Also, whenever you get an error, is
it is always helpful to report output of traceback
On Tue, Feb 16, 2010 at 6:50 PM, camelbbs camel...@gmail.com wrote:
Hi,
Can anyone help me for this error?
u-indexOf(cdf,6811818)
u
integer(0)
This tells you that there is no unit with name 6811818 in the
MoEx-1_0-st-v1,coreR1,A20080718,MR CDF file. You are simply asking
for information on
For your information:
The unit fragment length (UFL) and the unit genome position (UGP)
annotation files for the Affymetrix GenomeWideSNP_6 chip type has been
updated, and available at:
http://aroma-project.org/chipTypes/GenomeWideSNP_6
The source was the two Affymetrix NetAffx CSV files
Hi.
On Tue, Feb 9, 2010 at 7:40 PM, Randy Gobbel randy.gob...@gmail.com wrote:
I've just noticed in the past few days that with the new Web site,
it's not at all obvious how to download source files for the various
packages that go into aroma.affymetrix. I've managed it by pawing
through old
Hi Rama.
On Tue, Feb 9, 2010 at 10:15 AM, Rama Gullapalli
dr.ramachan...@gmail.com wrote:
Hi All,
First time poster, long-time lurker. Really appreciate all the wonderful
stuff you guys are doing (Henrik et al). Would love to be able to help in
anyway deemed necessary (Including documentation
On Thu, Jan 28, 2010 at 4:58 PM, branko b.miso...@lumc.nl wrote:
Hi all,
[snip]
4) Last one , regarding QC issue with plotting … SO when doing Array
(pseudo) image plots my RGui in windows complains e.g.:
If I do: cf - getFile (cs, 1)
plotImage(cf, transform=list(log2),
Hi.
On Tue, Jan 26, 2010 at 7:00 PM, parantu shah parantu.s...@gmail.com wrote:
Hi
I want to extract as ExpressionSet - the set of normalized array
(200+) aftter fitting the
plmEx - ExonRmaPlm(csN, mergeGroups=FALSE)
fit(plmEx, verbose=verbose)
[ not the chip effect or anything else]
I
Hi,
I managed to reproduce this when using the same names as you. It
turns out to be a bug causing indexOf(ds, foo+bar) of a data set
'ds' to return NA when the requested name contains a '+' symbol. The
reason was that the '+' was parsed as a regular expression symbol.
I've fixed R.filesets,
Hi,
On Thu, Jan 28, 2010 at 4:58 PM, branko b.miso...@lumc.nl wrote:
Hi all,
[snip]
3) Few questions regarding Quality checks and basic data
manipulations in Aroma:
[snip]
I ask this silly questions because Using R commands like str()
doesn’t show me the
object fields etc. so I
wonder which directory structure shall I create
and how to properly read the data for FIRMAGene processing.
Originally, I have 3 .cel files for one condition (M), and 3 .cel
files for another (S). Thank you! Mikhail.
On Jan 26, 6:58 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi
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