Hi.
On Fri, Oct 4, 2013 at 8:19 PM, Ann Loraine alora...@gmail.com wrote:
I am working with ATH1/GPL198 Affymetrix microarrays and would like to use
aroma to process a large set of arrays.
I'm following the vignette on this page:
http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis
Hi, thanks. Could you please give a more precise description what you
want to do, e.g. what other method and what to do after that?
/Henrik
On Fri, Aug 9, 2013 at 12:47 AM, Koray Doğan Kaya
koray.kaya.2...@alumni.boun.edu.tr wrote:
Hi,
I like Aroma Affy. However I want to use some external
Hi,
aroma.affymetrix v2.10.0 and friends has been released and is
available on CRAN (where the package is hosted). Update by:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
This release is mainly about bug fixes, internal cleanups and some
minor speedups.
Cheers,
coded. Please see:
https://groups.google.com/d/msg/aroma-affymetrix/r8CtCvdGWnE/jzQFMifxt2MJ
for more informations/details.
/Henrik
Thanks a lot for the help!
Sean
On Fri, Aug 2, 2013 at 11:03 AM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
On Thu, Aug 1, 2013 at 6
Hi Keith.
On Mon, Jul 29, 2013 at 5:47 PM, Keith Ching keithchi...@gmail.com wrote:
sorry if this has been fixed already..
i'm looking at a gene on chr9 at 138MB. I have segments that go out to
140MB.
But the ChromosomeExplorer plot is truncated at 134MB for a SNP6 chip.
Thanks for
On Mon, Aug 5, 2013 at 6:38 PM, Keith Ching keithchi...@gmail.com wrote:
Thanks Henrik this is working for me. I wasn't able to get it to recognize
the new file in annotationData/genomes/Human/
but I was able to change the default file in the package.
Did you try to rename it
?
Skip the exportTotalCnRatioSet() call, and instead use:
sm - CbsModel(dsTR, ref=dfR, tags=HapMapRef);
The 'tags' is just to add an informative tag to the output data set.
/Henrik
Thanks again for your help!
Sean
On Sun, Jul 28, 2013 at 4:28 PM, Henrik Bengtsson
henrik.bengts...@aroma
Hi.
On Fri, Jul 26, 2013 at 8:02 AM, sean nj njs...@gmail.com 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
Hi,
see http://aroma-project.org/howtos/ImproveProcessingTime
Most importantly, increasing the RAM option will make a big difference.
/Henrik
On Mon, Jul 15, 2013 at 11:05 PM, Ryan Chow clearlyconfus...@gmail.com wrote:
Hello,
I'm looking to process 4000 HG-U133_Plus_2 microarrays using
On Wed, Jun 12, 2013 at 9:56 PM, Wei Tang tangwei1...@gmail.com wrote:
Hi Henrik,
Would you tell me where I can find the information of human build for the
arrays?
it seems you used hg18? am I correct?
Which genome version you use depends on which annotationData/ files
you use. Here are the
] affyio_1.28.0 BiocInstaller_1.10.2 digest_0.6.3
preprocessCore_1.22.0 PSCBS_0.34.8
[6] zlibbioc_1.6.0
On Thu, Jun 20, 2013 at 2:29 PM, Henrik Bengtsson
henrik.bengts...@gmail.com wrote:
I thought I fixed this in aroma.core 2.9.2, but I guess it wasn't enough.
For now try
I thought I fixed this in aroma.core 2.9.2, but I guess it wasn't enough.
For now try to load the R.cache package on startup - that should work
around the problem. Let me know if it works.
Henrik
On Jun 20, 2013 5:46 PM, rangerq ranger...@gmail.com wrote:
Hi,
I got an error when I processed
of the PSCBS package.
/Henrik
Many thanks,
Wei
On Thu, Jun 6, 2013 at 5:38 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
On Thu, Jun 6, 2013 at 1:43 PM, Wei Tang tangwei1...@gmail.com wrote:
Everything goes very well. Nsp and Sty matched.
Great to hear.
BUT I forget
tools_3.0.0
On Wednesday, June 5, 2013 3:50:41 PM UTC-4, Henrik Bengtsson wrote:
Hi.
On Wed, Jun 5, 2013 at 11:31 AM, Wei Tang tangw...@gmail.com wrote:
Hi Henrik ,
Thank you for you suggestion.
but when I ran
res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp
On Wednesday, June 5, 2013 5:01:19 PM UTC-4, Henrik Bengtsson wrote:
On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang tangw...@gmail.com wrote:
Thank you, please see the info below.
script
dataSet_500K=EC500K
dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose
QuantileNormalization could affect the relationship between pairs of
coexpressed genes.
If not, could you suggest me another package I could use? Is limma my only
option ?
Looking forward hearing from you
Best
Jean-paul.
Le jeudi 13 août 2009 18:42:34 UTC+2, Henrik Bengtsson a écrit :
Hi
Hi Yadav,
thanks for reporting on this. It to me a while to reproduce it. A
quick fix would be to explicitly load the R.cache package, which is
the package that defines that missing getChecksum(). However, I've
fixed this in aroma.core v2.9.2, so you update the error should go
away. Update as
Hi all,
aroma.affymetrix v2.9.0 has been released and is available on CRAN
(where the package is hosted). Update by:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
This is mainly a maintenance update to meet some new CRAN
requirements. Interestingly, no bugs
to non-(list or vector) of type 'NULL'
2: In is.na(parent) :
is.na() applied to non-(list or vector) of type 'NULL'
list.files()
[1] HG-U133_Plus_2.cdf
On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote:
Hi.
On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED naw
- writeDataFrame(data, file=all_probes.txt,
header=list(chipType=getChipType(cdf)));
Again, not sure what you're going to use this for/where to import it;
you may end up reinventing the wheel.
Hope this helps
/Henrik
Thanks,
Jonathan
On Tuesday, April 23, 2013 2:40:56 AM UTC+2, Henrik Bengtsson
://groups.google.com/group/aroma-affymetrix/t/5a9fab682eebac1e
Henrik Bengtsson henrik.bengts...@aroma-project.org
Feb 13 01:48PM -0800
Hi Oscar,
I'm rather swamped right now, but just a few quick comments. Calling
so called copy-neutral segments via callNTCN() is a rather and
somewhat
I can reproduce this - very odd. I'll investigate a fix it. In the
meanwhile, install the aroma.* 2.8.0 versions via CRAN, e.g.
install.packages(aroma.core, repos=@CRAN@)
install.packages(aroma.affymetrix, repos=@CRAN@)
(Add repos=@CRAN@ to make sure not to install from other repositories.)
install
from R-forge, because that contains my non-official under-construction
and non-tested updates.
On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson
henrik.bengts...@gmail.com wrote:
I can reproduce this - very odd. I'll investigate a fix it. In the
meanwhile, install the aroma.* 2.8.0
:::genotypeOne() that needs to
be ported.
Anyway, thank you to share with us the aroma.affymetrix suite.
You're welcome - hopefully it makes everyday science a bit easier.
/Henrik
El viernes, 22 de marzo de 2013 19:31:10 UTC+1, Henrik Bengtsson escribió:
Hi Carles,
the quick answer
hbInstall() to never install from R-forge. FYI, don't install
from R-forge, because that contains my non-official under-construction
and non-tested updates.
On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson
henrik.bengts...@gmail.com wrote:
I can reproduce this - very odd. I'll
- verbose - Arguments$getVerbose(-8, timestamp=TRUE)
I've changed 'log' to 'verbose', because that will always work.
/H
Thx
Uma
On Sat, Mar 23, 2013 at 5:32 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
On Sat, Mar 23, 2013 at 2:29 PM, Uma Shankavaram
uma.shankava...@gmail.com
Hi Ingrid.
On Wed, Mar 20, 2013 at 4:45 PM, Ingrid Lönnstedt
ingrid.lonnst...@gmail.com wrote:
Hi!
I have segmented 56 SNP 6 tumour samples with segmentByNonPairedPSCBS(),
and like to call allelic balance segments with callAB() as required, I
understand, before I can call neutral TCNs with
Hi Carles,
the quick answer it that aroma.affymetrix only implements the CRLMM
method for the 100K (Mapping50K_Xba142 and Mapping50K_Hind142) and
500K (Mapping250K_Nsp and Mapping250K_Sty) chip types. For newer
methods you need to turn to the Bioconductor 'oligo' package.
However, what are you
Henrik Bengtsson henrik.bengts...@aroma-project.org
Feb 09 01:45PM -0800
Hi Oscar,
so you spotted a bug in the bootstrapping of the TCN mean-level
estimates. It only affected segments that had been called to be in
run-of-homozygosity (ROH) resulting in sampling from not all available
Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE
England
Please note that my email address will be changing to:
oscar.ru...@cruk.cam.ac.uk
Error in callAB (PSCBS)
http://groups.google.com/group/aroma-affymetrix/t/d066a381760d0543
Henrik Bengtsson henrik.bengts...@aroma-project.org
Hi,
sorry for the delay - I've been off the grid since two weeks.
On Thu, Jan 24, 2013 at 4:09 AM, Oscar Rueda oscar.ru...@cruk.cam.ac.uk wrote:
Dear all,
I'm trying to run PSCBS on 126 matched pairs, but only 60 of them have run
without errors. The last error I got was when running callAB:
Just to close this (old) thread:
On Mon, May 7, 2012 at 1:07 PM, sean nj njs...@gmail.com wrote:
Hi guys,
I tried to convert recent customCDF HTHGU133A_Hs_ENTREZG.cdf (version 15.10)
to binary format and end up with error message:
Error in convertCdf(HTHGU133A_Hs_ENTREZG.cdf,
Anderson
On Friday, January 4, 2013 3:48:03 PM UTC-6, Zheng Siyuan wrote:
you are right. Problem is solved after updating aroma.affymetrix to the
latest version.
Thank you
On Friday, January 4, 2013 3:15:55 PM UTC-6, Henrik Bengtsson wrote:
What's your session info after
Hi all,
aroma.affymetrix v2.8.0 has been released. Update by:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
Bug fixes, improved fault tolerance, more unique caching, improved
creation of CDF files from Bioconductor PDInfo packages and more. As
usual, details
On Fri, Dec 7, 2012 at 2:09 PM, Hooiveld, Guido guido.hooiv...@wur.nl wrote:
Hi,
Sorry for the indistinctness. You are correct; these are indeed R-packages
(CDF environments), thus not *files*. However, it won't be much effort to
also make them available as files. I/we will have a look at it
On Thu, Dec 6, 2012 at 5:54 AM, Maria Traka maria.tr...@ifr.ac.uk wrote:
Hi guys,
probably you've already given the answer somewhere but can i use
aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)?
Presumably the same way as 1.0 arrays?
I'm not working with those myself,
On Tuesday, 27 November 2012 21:40:54 UTC+2, Henrik Bengtsson wrote:
Hi,
this certainly looks weird and it's very puzzling. My last guess it
that your so called monocell CDF is corrupt (but I cannot see how that
happened). Verify that you get the same:
library(aroma.affymetrix);
cdf
At 2012-11-27 13:57:24,Henrik Bengtsson-4 [via aroma.affymetrix] [hidden
email] wrote:
Hi,
first thing to try whenever running out of memory in R is to retry in
a fresh R session. That often solves the problem. It's also useful
to know that all your aroma analysis is automatically stored
(units1);
int [1:945826] 935590 935591 935592 935593 935594 935595 935596 935597
935598 935599 ...
units - findUnitsTodo(plm);
str(units);
int [1:935589] 1 2 3 4 5 6 7 8 9 10 ...
On Monday, 26 November 2012 23:08:47 UTC+2, Henrik Bengtsson wrote:
On Mon, Nov 26, 2012 at 12:46 PM, Ioana
the latest version:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
you should also get aroma.core v2.7.1 [see
packageVersion(aroma.core)] and then both approaches work.
/Henrik
At 2012-11-28 03:11:25,Henrik Bengtsson-4 [via aroma.affymetrix]
[hidden email
, 26 November 2012 17:52:39 UTC+2, Henrik Bengtsson wrote:
Hi,
please provide the following information so I can help troubleshoot:
1. What's your sessionInfo() after doing library(aroma.affymetrix)?
2. Your complete script (right now I not sure which chip type your are
working on) up
Hmm... first run this in a fresh R session:
library(aroma.affymetrix);
cdf - AffymetrixCdfFile$byChipType(GenomeWideSNP_6, tags=Full);
csR - AffymetrixCelSet$byName(test, cdf=cdf);
acc - AllelicCrosstalkCalibration(csR, model=CRMAv2);
csC - process(acc, verbose=verbose);
bpn -
R.rsp_0.8.2R.cache_0.6.3
[10] R.devices_2.1.1R.filesets_1.1.5 digest_0.5.2
[13] R.utils_1.18.0 R.oo_1.10.1R.methodsS3_1.4.2
[16] e1071_1.6-1class_7.3-5
thanks,
rajesh
On Monday, November 19, 2012 11:04:15 AM UTC+5:30, Henrik Bengtsson wrote
Hi,
I've never seen that before, but remove any *.tmp or *.tmp.tmp etc
files and try again. If that does not work, then please
1. show your script exactly at it is,
2. show the output you get from
library(aroma.affymetrix);
sessionInfo();
/Henrik.
On Sun, Nov 18, 2012 at 8:02 PM, Raj
Hi,
sorry about that - a hiccup of mine (I've been slowly pushing updates via
the aroma server and am now pushing them to CRAN and I missed a bit here).
Retry with:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
and it should work.
/Henrik
On Thu, Oct 25, 2012 at
Hi,
thanks for reporting and sorry about this - a hiccup of mine (I've
been slowly pushing updates via the aroma server and am now pushing
them to CRAN). Retry with:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
and it should work. If not, please let me know.
Hi,
more comments below.
On Fri, Oct 19, 2012 at 3:37 AM, Laurent Malvert lmalv...@idbs.com wrote:
from: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
On Thu, Oct 18, 2012 at 5:50 AM, Laurent Malvert lmalv...@idbs.com wrote
Hi,
your CDF is most likely corrupt. You didn't tell us what
cdf - AffymetrixCdfFile$byChipType(HTHGU133A_Hs_ENTREZG);
print(cdf);
outputs, and also not how you obtained that CDF. However, it looks
like (it originates from) a custom CDF by the BrainArray project
Hi.
On Thu, Oct 18, 2012 at 5:50 AM, Laurent Malvert lmalv...@idbs.com wrote:
Hello Henrik and Aroma Affymetrix users,
I understand you have been in contact with Jay over the integration of
ArrayExplorer within our products, since the last time I wrote to you.
He reported to me some
!
Martina
Il giorno lunedì 24 settembre 2012 19:55:51 UTC+2, Henrik Bengtsson ha
scritto:
On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen
clausli...@gmail.com wrote:
Hi,
Last week I ran CRMA (v2): Paired total copy number analysis
Using the following annotation files
Hi, sorry about the affxparser mess.
See if the following
source(http://aroma-project.org/affxparser.R;);
installAffxparser();
solves your problems. The above will run tests to make sure
everything works fine and if it says that is the case, you're read to
rock'n'roll.
Please report back and
On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen
clauslindbj...@gmail.com wrote:
Hi,
Last week I ran CRMA (v2): Paired total copy number analysis
Using the following annotation files
GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
Hi.
On Wed, Sep 19, 2012 at 5:36 AM, S. A. Haider shazi...@gmail.com wrote:
Hi Guys,
Following preprocessing (doCRMAv2), i am running segmentation using CBS. I
have few hundreds of samples (~600 SNP6) and as far as i understand, aroma
tries to keep memory usage to minimum. So far, it looks
LRR are basically log2 CN ratios centered around 0 whereas CT are
non-logged CN ratios centered around 2 (or whatever you think the
ploidy is), so CT = 2^LRR should do.
/H
On Tue, Sep 18, 2012 at 6:28 AM, Reed ghosh...@gmail.com wrote:
I am trying to run segmentByPairedPSCBS on my illumina 1M
HI, you need to give us way more information in order to help. Right
now your question is like My car used to run well but not any longer
- what's wrong with it?
FYI, we run extensive redundancy tests for each update to make sure we
are not breaking anything, so most likely you're not experience
position.
Yes, nothing in the TumorBoost method makes use of genomic locations
(nor chromosome or position); it normalizes tumor BAFs given the
corresponding matched normal BAFs for SNPs independently of each
other.
/H
Reed.
On Thursday, September 13, 2012 9:36:34 PM UTC+5:30, Henrik Bengtsson
much what you do, because this only affects a teeny fraction of the
data you have.
/Henrik
Thanks,
Mike
On Friday, September 14, 2012 5:00:42 PM UTC-4, Henrik Bengtsson wrote:
On Fri, Sep 14, 2012 at 1:57 PM, Mike michael...@gmail.com wrote:
I am using aroma.affymetrix for pre-processing
, a data frame and then pass those values to
normalizeTumorBoost().
/Henrik
Please help.
Reed
On Wednesday, September 12, 2012 8:14:21 PM UTC+5:30, Henrik Bengtsson
wrote:
Hi,
On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap uny...@gmail.com wrote:
Hello,
I have a question regarding
Hi,
On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap unya...@gmail.com wrote:
Hello,
I have a question regarding to TumorBoost.
I have data from Affymetrix (GenomeWideSNP_6) and Illumina (Omni1-Quad) for
the same set of samples.
I want to do normalization of CNV for the data from both
Hi.
On Wed, Sep 12, 2012 at 6:07 AM, Maria Rodrigo mrod...@gmail.com wrote:
Hi,
I have come across an error when extracting probe intensities from the exon
array using function getUnitIntensities()
Error in readCelUnits(pathnames, cdf = cdfUnits, readStdvs = FALSE,
readPixels = FALSE, :
Hi,
aroma.affymetrix v2.6.0 is available. Update by running:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
This release consists mostly of internal framework improvements and
only a few minor updates for the end user, e.g. improvement of the
bpmapCluster2Cdf()
On Thu, Sep 6, 2012 at 10:09 AM, Mike michael.gorm...@gmail.com wrote:
I am trying to install in R.12.1. Is this causing the problem?
That's certainly possible, yes. Although I try not to restrict the
code/packages to require the very latest versions of R, I do *not*
validate that they
version of R solved my installation problems.
Thanks,
Mike
On Thursday, September 6, 2012 2:31:52 PM UTC-4, Mike wrote:
Thanks Henrik. I'll post back once I upgrade to let the community know
whether this solved my issues or not.
On Thursday, September 6, 2012 2:12:28 PM UTC-4, Henrik
by
first downloading to a temporary file, which is only renamed when the
download is complete. Just as most modern downloader are doing, e.g.
web browsers.
/Henrik
Thank you very much for your help!!
Best,
María
On 29 August 2012 21:37, Henrik Bengtsson
henrik.bengts...@aroma-project.org
)
Package: affxparser
Version: 1.28.1
Date: 2012-03-30
Title: Affymetrix File Parsing SDK
Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper
Daniel Hansen, Martin Morgan
Maintainer: Kasper Daniel Hansen khan...@jhsph.edu
Description: Package for parsing Affymetrix files
On Wed, Aug 29, 2012 at 6:38 AM, Jay jayangshu.s...@gmail.com wrote:
Hi Henrik,
Hope you are doing good. Firstly, thank you very much for your reply.
I am extremely sorry for not attaching the screenshot. I am attaching it now.
Please do let me know if you have any issue viewing this jpeg.
;);
/Henrik
On Wed, Aug 29, 2012 at 11:52 AM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Ok, there is something wrong with your downloads. Downloading that URL
should give you a file that is exactly 40,108,891 bytes. Your
downloaded file is of a different size. I don't know how
: 18708
## Cells per unit: 350.31
## Number of QC units: 1
On 27 August 2012 02:09, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi,
I see nothing wrong with your script. I suspect that the CDF you've
downloaded got corrupted or something. Do you get the same output
On Wed, Aug 1, 2012 at 11:31 AM, Fong fongchunc...@gmail.com wrote:
Hi,
I seem to be unable to figure out whether this question has been addressed
or not so I apologize if this has already been asked. Basically I have a
set of U133 arrays which I have processed through aroma.affymetrix and
Hi,
I'm not sure what is going on. It should certainly not get stuck for
14 hours, unless you're running out of RAM and you're swapping like
crazy, but that should not happen if you have, say, at least 1GB of
RAM. Are you doing this in a fresh R session?
Where it seems to hang has nothing to
Hi,
I see nothing wrong with your script. I suspect that the CDF you've
downloaded got corrupted or something. Do you get the same output as
below:
library(aroma.affymetrix)
cdf - AffymetrixCdfFile$byChipType(chipType, tags = coreR3,A20071112,EP);
cdf
## AffymetrixCdfFile:
## Path:
Hi,
it could be either a bad array or corrupt annotation files. I don't
know which UFL annotation data file you are using, but I recommend
that you download the most recent one from
http://aroma-project.org/data/annotationData/chipTypes/Mapping50K_Hind240/
and then confirm that you get:
Just a mistake. Thanks for spotting it. /Henrik
On Mon, Jul 23, 2012 at 4:36 PM, complexkid tejalonl...@gmail.com wrote:
Hi Henrik,
I just noticed your response in the thread :
https://groups.google.com/forum/#!msg/aroma-affymetrix/RCHLDIfO47s/SJafAcaQnZsJ.
Why is the following operation done
Hi.
On Wed, Jul 11, 2012 at 9:59 AM, Nir n...@broadinstitute.org wrote:
HI All,
I am trying to run the standard procedures for a HuGene-1_0-st-v1 array.
Here is the code:
---
setwd(my work dir ...);
library(aroma.affymetrix)
This is most likely unrelated to the aroma framework and more likely
to be related to a setup issue with one of your PNG device drivers.
To troubleshoot, what does the following output give if you start a
fresh R session:
library(aroma.core);
pngDev - findPngDevice(transparent=FALSE, force=TRUE);
On Tuesday, June 26, 2012 11:51:49 PM UTC-4, Henrik Bengtsson wrote:
Following the troubleshooting of annotationData/ on
http://aroma-project.org/troubleshooting/DirectoryStructures using
chipType - GenomeWideSNP_6, what does print(list.files(path=path))
output?
/Henrik
On Tue, Jun 26
You can ignore them. Warnings are almost always alright - errors are not.
/Henrik
On Tue, Jun 19, 2012 at 6:40 AM, NT_CMU nitesh.tur...@gmail.com wrote:
Thank you Henrik and Pierre. I am able to run it successfully now.
It gives me a few warnings at the end.
warnings()
Warning messages:
On Mon, Jun 18, 2012 at 1:59 PM, NT_CMU nitesh.tur...@gmail.com wrote:
Hi
Thanks for the help Pierre. I managed to resolve it. I am just using the
AffymetrixCelSet$byName with the cdf information instead of the chipType.
For some reason, that still refuses to work.
These are the two possible
Hi,
you should also get the following annotation files:
annotationData/
chipTypes/
GenomeWideSNP_6/
GenomeWideSNP_6,Full,*.acs
GenomeWideSNP_6,Full,*.ugp
GenomeWideSNP_6,Full,*.ufl
as explained in for instance
http://aroma-project.org/vignettes/CRMAv2. You can get them from
Hi.
On Thu, Jun 14, 2012 at 11:42 PM, Tommaso Mazza mazza.tomm...@gmail.com wrote:
Hi All,
this is a trivial question for sure, but please give me an hint.
I have data from the chip in object and from a Genome-Wide Human SNP Array
6.0 - Affymetrix and a GeneChip Human Mapping 250K array.
I
conversions have done before so everything should be ok.
/Henrik
On Wed, Jun 13, 2012 at 5:24 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi.
On Tue, Jun 12, 2012 at 1:17 AM, dave davidarteta2...@gmail.com wrote:
Hi,
I hope I am not asking a too simple question but I am trying
Hi.
Yes, to extract all cell (=probe) intensities from all arrays in an
AffymetrixCelSet ('csN'), you can do:
Y - extractMatrix(csN, drop=FALSE)
Typically an Affymetrix array contains several million probes, so this
will be a rather big matrix, especially if you have many arrays.
More comments
Hi.
On Wed, Jun 6, 2012 at 9:23 AM, Hyuna Yang hyunay...@gmail.com wrote:
Hi all,
I have custom array (similar to human Exon array) and try to study
alternative splicing using FIRMA.
i) in theory, I think I can use FIRMA, but wonder that's possible at current
aroma.affymetrix setup.
Yes,
we write them on a xls file
after PSCBS?
Thank you in advance...
Happy new year :)
2011/12/31 Henrik Bengtsson henrik.bengts...@aroma-project.org
Hi Zehla,
this is most likely yet another thing caused by the fact that their
code overrides the methods of aroma.affymetrix
Hi.
On Tue, May 8, 2012 at 4:16 AM, Jay jayangshu.s...@gmail.com wrote:
Dear Henrik
I am a consultant working with Laurent Malvert.
Many thanks for helping us with the aroma.affymetrix issue we have
been experiencing. Gladly this looks like being complete.
Whilst installing your recent
Hi.
On Fri, May 18, 2012 at 11:17 AM, sean nj njs...@gmail.com wrote:
Hi, it's me again :)
I have some level 2 TCGA agilent CGH 244A data, the text files of log2
ratios. I followed vignettes (http://aroma-project.org/node/43 and
http://www.aroma-project.org/node/88) and created UGP files and
Hi.
On Mon, Apr 30, 2012 at 5:31 AM, Marcin kke...@gmail.com wrote:
Dear Henrik,
I have a dataset in which my collaborators took two types of cancer
cell lines and made a few single copy clones of them per cell line.
The clones were then used for drug resistance study in pairs (i.e.
clone
Hi.
On Sat, May 5, 2012 at 1:12 PM, Sathish Periyasamy
sathish.periyas...@gmail.com wrote:
I have completed the doCRMAv2 for tumour/ Normal pairs and obtained
the results in ChromosomeExplorer. However, I would like to find the
common variance (i.e. gains and loss, LOH) across these pairs.
Hi,
everything is fine; you've got the correct annotation data files. The
only issue is that code writing that 'url' column added to the
regions.xls file is rather stupid, i.e. the genome version is hard
coded.
You can rewrite the regions.xls file with the correct UCSC Genome
Browser by passing
Hi,
some minor corrections/clarifications below.
On Mon, Apr 16, 2012 at 1:32 AM, Pierre Neuvial
pie...@stat.berkeley.edu wrote:
Hi Andy,
On Mon, Apr 16, 2012 at 4:15 AM, Andyusa andrew.wang.2...@gmail.com wrote:
HI All,
It was my first time to use the aroma to run two pairs of samples vs
aroma.apd_0.2.0
R.huge_0.3.0
[5] aroma.core_2.4.6 aroma.light_1.22.0 matrixStats_0.4.4
R.rsp_0.7.3
[9] R.cache_0.6.1 R.filesets_1.1.4 digest_0.5.2
R.utils_1.12.0
[13] R.oo_1.9.3 R.methodsS3_1.2.2
Am Freitag, 6. Januar 2012 14:44:00 UTC+1 schrieb Henrik
Hi,
first of all, there is a very simple reason for this, we just have to
find out why. My best guess now is that one of the files are
incomplete. Start a fresh R session and verify that you get the
exactly same *file sizes* as below:
library(aroma.affymetrix);
cdf -
...and by the way, what is your sessionInfo(), i.e. what does the
following report?
library(aroma.affymetrix);
sessionInfo();
/Henrik
On Thu, Apr 5, 2012 at 1:55 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi,
first of all, there is a very simple reason for this, we just
Hi.
On Wed, Apr 4, 2012 at 7:57 AM, Fred Foucault
frederic.fouca...@gmail.com wrote:
Hello,
I want to get allele specific copy number from SNP6 CL files
I´m following the vignette for ACNE.
I installed the annotation data in \test\annotationData\chipTypes
\GenomeWideSNP6.0
The name of
Hi,
aroma.affymetrix v2.5.0 and friends have been updated. Update by running:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
The main update in this release is on the ArrayExplorer v3.4 and
ChromosomeExplorer v3.4, which can now be viewed (both locally and
online)
Hi.
On Mon, Mar 19, 2012 at 12:02 PM, Fong fongchunc...@gmail.com wrote:
Hi,
I am using SNP6 arrays right now and I've got an annotationData directory
that looks like this:
GenomeWideSNP_6,Full.cdf
GenomeWideSNP_6,Full,monocell.CDF
GenomeWideSNP_6,HB20080710.acs
Hi,
sorry for the delay.
To me it looks like you cannot install any of the packages that are on
CRAN (= 'DEFAULT' in the output). First, try to install 'digest' as
follows:
install.packages(digest)
Verify that it works by loading it, i.e. library(digest). If it
still doesn't work, please
Hi,
sorry for the delay on this one. It is seems that you have a special
case that we didn't consider when we designed the naive genotyping
algorithm. I can have a look at this, but in order to do that I'd
need some example data. Would you mind making the data for one
tumor-normal pair
creating this file?
Thanks a lot.
Yu
On Mon, Mar 5, 2012 at 10:15 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
20 data files should be no problems. I'm still quite sure that you
have '#' in your generated column names. Could you send a file
containing the first 30 rows
Hi Laurent.
On Thu, Mar 8, 2012 at 6:13 AM, Laurent Malvert lmalv...@idbs.com wrote:
On Thursday, February 2, 2012 4:47:34 AM UTC, Henrik Bengtsson wrote:
[...]
When time permits, I'll also update ArrayExplorer (which still only
works in Firefox 3.x).
Hello Henrik,
I am unfamiliar
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