Hi.
On Wed, Nov 16, 2011 at 12:06 PM, Kai wangz...@gmail.com wrote:
Hi Henrik,
For GWS6 data it seems to me that they can be processed to generate
either an AromaUnitTotalCnBinarySet or a CnChipEffectSet. For
example, codes in your vignette Estimation of total copy numbers
using the CRMA v2
Hi,
I'd suggest that you use the Paired PSCBS segmentation method and the
LOH caller proposed in the PSCBS paper:
A.B. Olshen*, H. Bengtsson*, P. Neuvial, P. Spellman, R.A. Olshen,
V.E. Seshan, Parent-specific copy number in paired tumor-normal
studies using circular binary segmentation,
On Nov 16, 5:09 pm, Henrik Bengtsson henrik.bengts...@aroma-
project.org wrote:
Hi.
On Wed, Nov 16, 2011 at 12:06 PM, Kai wangz...@gmail.com wrote:
Hi Henrik,
For GWS6 data it seems to me that they can be processed to generate
either an AromaUnitTotalCnBinarySet or a CnChipEffectSet
Hi,
I'm digging through my inbox and found this one - sorry for wait.
On Tue, Oct 18, 2011 at 12:54 PM, rahul v.rahul.sim...@gmail.com wrote:
Hello Henrik,
I have a custom CDF for HuEx1.0stv2 and each probeset represents an
exon. I am confused with mergeGroups option in ExonRmaPlm.
When
Hi,
sorry for the wait.
On Fri, Oct 14, 2011 at 6:25 AM, rene.rotterdam
rene.boettche...@googlemail.com wrote:
Hi everyone,
I have a weird situation at the moment, as I am processing my HuEx
chips according to your suggested script and all columns in the
fsScores array contain -processed
Hi.
On Tue, Oct 18, 2011 at 2:46 AM, rene.rotterdam
rene.boettche...@googlemail.com wrote:
Hi everyone,
in my group the question popped up whether it is possible to perform
the FIRMA analysis on a subset of a number of samples that have been
normalized all together.
For example: Assume we
Congratulations - you just won the price for the world shortest issue report ;)
Some ideas:
1. Use argument verbose=-10
2. Use traceback() when you get an error.
Other than that:
3. What is your sessionInfo()?
4. Show us your script.
/Henrik
On Tue, Nov 29, 2011 at 11:57 PM, Peiyong
limma_3.10.0
[16] affy_1.32.0 Biobase_2.14.0
loaded via a namespace (and not attached):
[1] affyio_1.22.0 BiocInstaller_1.2.1 preprocessCore_1.16.0
[4] tools_2.14.0 zlibbioc_1.0.0
On Wed, Nov 30, 2011 at 4:05 PM, Henrik Bengtsson
henrik.bengts...@aroma
On Wed, Nov 30, 2011 at 2:12 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi.
NO REPLY EXPECTED
The above sentence was a mistake - seems to been added by my email
client. Feel free to reply. /H
On Wed, Nov 30, 2011 at 12:24 AM, Peiyong jiangpeiy...@cuhk.edu.hk wrote
Hi.
On Thu, Dec 1, 2011 at 12:40 PM, Steven McKinney smckin...@bccrc.ca wrote:
Hi all,
I am setting up to run analysis on Affymetrix SNP6, 250K Nsp and 250K Sty
chip types.
As I read through the current documentation, I've noticed the following items
that
may need attention, or I might
Hi.
On Wed, Nov 30, 2011 at 6:38 PM, xiaowei guan xwei.g...@gmail.com wrote:
Hello Henrik,
May I ask you a question about using the http://www.aroma-project.org/node/38
Vignette to derive the gene centric values for HuGene-1_0-st-v1 array? I
follow the command, but it only generated the
Hi.
Yes, the Aroma framework can handle this.
On Fri, Dec 2, 2011 at 12:19 PM, Steven McKinney smckin...@bccrc.ca wrote:
Hi all,
I am running an analysis on Affymetrix SNP6, 250K Nsp and 250K Sty chip types.
For various reasons, patient samples were assessed either on SNP6 chips or
on 500K
.
Steven McKinney
-Original Message-
From: aroma-affymetrix@googlegroups.com [mailto:aroma-
affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: December-02-11 12:49 PM
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Combining data from multiple chip
writeDataFrame(), cf. http://aroma-project.org/howtos/writeDataFrame.
/Henrik
On Thu, Dec 1, 2011 at 6:14 AM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
On Wed, Nov 30, 2011 at 2:12 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi.
NO REPLY EXPECTED
Hi.
On Tue, Dec 6, 2011 at 11:49 AM, Steven McKinney smckin...@bccrc.ca wrote:
Hi all,
Data from multiple sources is available that would in principle allow
me to do a tumour/normal copy number analysis. The normal data was
obtained from samples processed using Affymetrix GenomeWideSNP_6
Hi,
On Mon, Dec 12, 2011 at 1:15 PM, Greg Wall greg.d.w...@gmail.com wrote:
CORRECTION:
ref.theta - extractMatrix(Normal)
theta - extractMatrix(Tumor)
C - 2 * theta/ref.theta
On Mon, Dec 12, 2011 at 1:09 PM, Gregory W greg.d.w...@gmail.com wrote:
Hello,
Many thanks for
@googlegroups.com [aroma-affymetrix@googlegroups.com]
On Behalf Of Henrik Bengtsson [henrik.bengts...@gmail.com]
Sent: December 2, 2011 12:48 PM
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Combining data from multiple chip types
Hi.
Yes, the Aroma framework can handle
On Tue, Dec 13, 2011 at 2:44 AM, James F. Reid
james.r...@ifom-ieo-campus.it wrote:
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You
Hi.
On Tue, Dec 13, 2011 at 7:48 AM, wisekh6 wise...@gmail.com wrote:
Dear Henrik,
I ran doCRMAv2 with copy number data on the GenomeWide SNP6.0
platform.
For your information, all annotation files used in this run were
downloaded from your website, and R 2.13.0 was loaded.
This run
Hi.
On Tue, Dec 13, 2011 at 1:50 PM, Steven McKinney smckin...@bccrc.ca wrote:
-Original Message-
From: aroma-affymetrix@googlegroups.com [mailto:aroma-
affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: December-12-11 9:30 PM
To: aroma-affymetrix@googlegroups.com
...done
20111216 13:09:45| Compiling ChromosomeExplorer.onLoad.js.rsp...done
20111216 13:09:45|Generating ChromosomeExplorer report...done
Thank you for helping me :)
2011/12/16 Henrik Bengtsson henrik.bengts...@aroma-project.org
Hi.
On Fri, Dec 16, 2011 at 12:17 AM, Zelha Nil zelh
Hi Minya,
what does sessionInfo() report after library(PSCBS)?
Also, could you please send me (offline; not to the mailinglist) the
following 'MP20120106.Rbin' file:
df - data.frame(chromosome=chromosome, x=x, CT=CT, betaT=betaT,
betaN=betaN);
saveObject(df, MP20120106.Rbin);
/Henrik
On
Hi David,
I've created ACS, UFL and UGP files for the CytoScanHD_Array chip type, but
they are still to be validated. You could start by comparing the content
of yours to mine, which you find at:
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/incomplete/
/Henrik
Hi David,
it may be that your ACS file (containing probe sequences) is corrupt. What
do you get if you do:
acs - getAromaCellSequenceFile(cdf);
data - getSnpNucleotides(acs, verbose=-50);
The you should see what 'uPos' outputs. It holds the (unique) set of
nucleotide positions identified in
BTW, there is no full CDF for this chiptype; Affymetrix
provides only the CytoScanHD_Array.cdf. The concept of a default and
full CDF was only for GenomeWideSNP_5 and GenomeWideSNP_6, which
basically because after settling on the chip design, Affymetrix discovered
that some probes/SNPs didn't
Hi,
with help of the data you sent me, I could reproduce the issue,
identify and correct the bug. Update to PSCBS v0.19.4:
http://cran.r-project.org/web/packages/PSCBS/
Let me know if it solved it for you
/Henrik
On Fri, Jan 6, 2012 at 5:43 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote
Yes,
the process is basically the same; replace AromaUnitTotalCnBinaryFile
with AromaUnitFracBCnBinaryFile. Put the TCN and the BAF data files
in the same directory. The BAF files should have the same name as the
TCN files but with an *,fracB.asb suffix. The use of
AromaUnitFracBCnBinaryFile is
Hi,
I didn't get around to fix that in aroma.* v2.4.0. The only thing I
can say now is to hack (read update) the GLAD package and update its
cytoband data. For instance, you can load that data by:
pathname - system.file(data/cytoband.RData, package=GLAD);
keys - load(pathname);
keys
[1]
Sorry,
that should have been:
acs - getAromaCellSequenceFile(cdf);
cells - getAlleleCellPairs(cdf, verbose=verbose);
data - getSnpNucleotides(acs, cells=cells, verbose=-50);
Look for the Unique SNP positions: output.
/Henrik
On Sun, Jan 8, 2012 at 3:23 PM, D Goode dgoode.stanf...@gmail.com
Ok, so it fails to identify any SNP positions based on your ACS file, cf.
SNP positions:
int [1:2410205] NA NA NA NA NA NA NA NA NA NA ...
Tabulated SNP positions:
character(0)
Unique SNP positions:
integer(0)
My guess is that your ACS file is incorrect (all zeros?). Did you
compare
Hi,
I finally got around to have a serious take at this and you're correct it
does no longer retrieve cytoband information from the GLAD package.
Instead it looks for a cytoband data file:
annotationData/genomes/genome/genome,cytobands(,tag)*.txt
In the aroma.core package, it will always find
,HB20111008.acs
dgoode$ wc CytoScanHD_Array,HB20111008.acs
2 11 179217220
annotationData/chipTypes/old/CytoScanHD_Array,20120104.acs
I'll try building the acs again. In the meantime, is it safe to use yours?
Cheers,
David
On Friday, 13 January 2012 15:55:25 UTC+11, Henrik
Hi, this message only applies users of OSX 10.6 (Snow Leopard) or
OSX 10.7 (Lion) running R v2.14.0 or newer.
It has been reported that if one (i) on R v2.14.0, (ii) on OSX 10.6 or
10.7, (iii) install the *binary* build of affxparser v1.26.2 by
Bioconductor, then affxparser causes R to crash
, Jan 13, 2012 at 4:31 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi,
I could reproduce this using the PairedPSCBS object that you sent me;
library(PSCBS);
# Load Paired PSCBS results with AB calls already done
fit - loadObject(HoonKim_20120110.Rbin);
fitC - callLOH
On Sun, Jan 15, 2012 at 11:20 AM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
On Sat, Jan 14, 2012 at 10:02 PM, Hoon Kim wise...@gmail.com wrote:
Dear Henrik,
Thank you very much for your time to reply to my questions, and your
suggestions worked very well. By following your
a theoretical as well as a practical point of
view. The complication of LOH is unfortunately rarely appreciated and
often overlooked in most of the literature.
/Henrik
Again, thank you very much, and have a good holiday.
Best,
Hoon Kim
On Sun, Jan 15, 2012 at 1:20 PM, Henrik Bengtsson
Since there are several different PNG drivers for R, aroma tries to
automatically find one that works. Try the following in a fresh R
session:
library(aroma.core);
pngDev - findPngDevice(transparent=FALSE);
pngDev(foo.png, width=840, height=640); plot(1:10); dev.off();
Is foo.png empty? What
Hi,
the loading of the Cairo package is misleading here, since it is
actually not utilizing it. (In the next version of aroma.core, the
Cairo package will not be loaded unless really needed). Instead,
print(pngDev)
function (...)
pngTyped(..., type = cairo)
environment: 0x103f64b88
tells
On Wed, Jan 18, 2012 at 1:36 AM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi,
the loading of the Cairo package is misleading here, since it is
actually not utilizing it. (In the next version of aroma.core, the
Cairo package will not be loaded unless really needed). Instead
Hi.
On Wed, Jan 18, 2012 at 12:53 PM, Steven McKinney smckin...@bccrc.ca wrote:
Thanks Henrik
Answers in-line below, and full output at end.
-Original Message-
From: aroma-affymetrix@googlegroups.com [mailto:aroma-
affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent
You need to update aroma.affymetrix. The version you are using is
from July 2010.
Thanks for the note about sfit and 64-bit machines. I'll add it to the
list of things to look at.
/Henrik
On Thu, Jan 19, 2012 at 2:48 AM, Maxime Tarabichi galder@gmail.com wrote:
Hi,
I have a problem when
Hi.
On Thursday, January 19, 2012, Kai wrote:
Hi Henrik,
In the vignette http://www.aroma-project.org/node/88;, the LRR data were
stored under rawCnData, but it seems to me that in recent updates you have
created a new sub-directory called totalAndFracBData - what are the
difference
);
/Henrik
What am I doing wrong?
On Jan 20, 3:57 am, Henrik Bengtsson henrik.bengts...@aroma-
project.org wrote:
You need to update aroma.affymetrix. The version you are using is
from July 2010.
Thanks for the note about sfit and 64-bit machines. I'll add it to the
list of things to look
pm, Henrik Bengtsson henrik.bengts...@aroma-
project.org wrote:
Hi.
this is odd, but there is for sure a simple explanation to it. Let's
find out. I have my suspicions, but before moving to the next step,
what does the following report:
sm - CbsModel(ds2);
cesTuple - getSetTuple(sm
*theta/thetaR) as well as CN intensity
(theta). By adding tags we try to make this less ambiguous.
/Henrik
Thank you for sharing your experience.
Best,
Kai
On Friday, January 20, 2012 6:37:25 PM UTC-8, Henrik Bengtsson wrote:
Also in the same vignette, the TotalCnBinary files are named
Hi,
first, I apologies that you had problems post your message; I just
noticed that there were several messages on hold to be approved by
the moderators. Normally we get a notice about this, but for some
reason we didn't get it. Now to your question...
On Fri, Jan 27, 2012 at 12:17 AM,
Hi,
I've uploaded aroma.core v2.4.5 which now includes the missing
require.js file. In a *fresh R session* (R -vanilla), do:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);
When doing setup(ce, force=TRUE), with 'ce' being an(y)
ChromosomeExplorer object, it will
?
Kind regards,
Angelina
From: aroma-affymetrix@googlegroups.com [aroma-affymetrix@googlegroups.com]
On Behalf Of Henrik Bengtsson [henrik.bengts...@aroma-project.org]
Sent: 02 February 2012 05:05
To: aroma-affymetrix@googlegroups.com
Subject: Re
Hi,
originally those data files were only available on a DVD that you had
to order from Affymetrix, whereas now you'll find *similar* data files
from the the HapMap Project itself. AFAIK, we are not allowed to
redistribute. Even if you cannot find the exact same samples at
HapMap, you can use
Hi,
I suspect you're asking for something that is not possible, so can you
clarify/define what you mean by mutations?
/Henrik
On Sun, Feb 12, 2012 at 5:06 PM, sigrid sigrid.ro...@gmail.com wrote:
Hi,
I have successfully run TumorBoost on my samples. I would like to
retrieve the mutations
On Sun, Feb 12, 2012 at 5:18 PM, sigrid sigrid.ro...@gmail.com wrote:
Hello,
I would like to know if my tumor sample is mutated compared to my
normal sample for a specific gene.
Do you mean mutations of individual nucleotides?
/Henrik
Thank you!.
Sigrid
On 13 fév, 09:10, Henrik
(rawData/C11/GenomeWideSNP_6/)
Many thanks,
Angelina
From: aroma-affymetrix@googlegroups.com [aroma-affymetrix@googlegroups.com]
On Behalf Of Henrik Bengtsson [henrik.bengts...@aroma-project.org]
Sent: 10 February 2012 19:50
To: aroma-affymetrix
Hi.
On Tue, Feb 28, 2012 at 3:46 AM, Saif UrRehman saif.urreh...@icr.ac.uk wrote:
Hi guys,
I am trying to normalise 5000 HG-U133A celfiles using the aroma library it
seems to run fine.
However it stopped reading in Celfiles after 2,246 files after about 11
hours. It appears to fail
Hi.
On Fri, Mar 2, 2012 at 8:52 AM, Yu Song ys...@oakland.edu wrote:
Dear Mr.Bengtsson,
I am trying to create a data containing the unitName, chromosome
and position from the output CEL of preprocessing.
What type of CEL files? What type of preprocessing?
/H
Is there a certain command to
Hi.
On Fri, Mar 2, 2012 at 1:37 AM, hiberbear xshin...@gmail.com wrote:
Hi everyone:
I am running aroma.affymetrix on human exon array (HuEx-1_0-st-v2). I find a
confusing thing about the gene summary:
trFit is identical to ExFit.
My understanding is that if mergeGroups=TRUE, I may get a
patients(20)?
Thanks a lot for your help!
Yu
On Mon, Mar 5, 2012 at 2:29 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi Yu,
the quick answer is that your file has been successfully written, but
depending on where you're loading it, the column names may not be
correctly parsed
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
On Fri, Mar 9, 2012 at 11:40 AM, Gregory W greg.d.w...@gmail.com wrote:
From trial and error I see I can simply use the function:
AromaUnitTotalCnBinarySet()
and pass it my list of files.
Yes, i.e.
files - list(...);
ds - AromaUnitTotalCnBinarySet(files);
(I think) you can also create an
-
On Fri, Mar 9, 2012 at 1:08 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi.
I see, the instructions I gave you before did not write copy numbers
*relative to a reference*, but copy number *signals as-is* (=on a
non
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
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,
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
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,
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
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.
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.
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 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,
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 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
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
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 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
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);
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)
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
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:
: 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
)
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
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
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
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()
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, :
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