Thanks for reporting. Retry with:
if (.Platform$OS.type == "windows") options(url.method = "libcurl")
source("https://callr.org/install#aroma.affymetrix;)
We've updated the online installation instruction accordingly.
On Thursday, October 31, 2019 at 6:06:43 AM UTC+1, Sreya Mukherjee
Dear Peter,
First, just to make sure we are talking about the same things, when
you write "I have applied ASCRMA to each array separately.", you mean
that you applied ASCRMA(v2) to each of the two *batches* separately,
right ? In the aroma-project world, we usually reserve the word
'array' for
Hi Z.,
If you want people to be able to help you out, then you need to
explain exactly what you did. Can you report the output of
sessionInfo() and traceback(), and post a complete code example ?
Have you checked that your problem is not already solved in the other
threads titled Cannot fit
Hi,
You can start by the website of the Aroma project:
http://www.aroma-project.org/
In particular, see the get started tab on the left.
Pierre
On Thu, Jan 16, 2014 at 2:20 PM, Fernando Andrade fernand04ndr...@gmail.com
wrote:
Hello, this is my first time using aroma.affymetrix, and I'm
Hi Emilie,
It's certainly possible to do this within the Aroma framework (e.g. using
the function binnedSmoothing). It's probably not as straightforward as
running the segmentation directly, though, because this is not a typical
use case.
In fact, I'm not sure why you want to perform smoothing
. Instead, let your working directory be something
like:
C:/Users/nwayyin/AromaAnalysis/
and let that be your working directory in R.
/Henrik
why this error occur please if you know the cause of problem
please
tell me
On Tuesday, April 30, 2013 3:16:00 PM UTC+1, Pierre Neuvial
Hi,
This thread should help you solving your problem:
https://groups.google.com/forum/?fromgroups=#!topic/aroma-affymetrix/S_wLLGcU8S0
Cheers,
Pierre
On Fri, Jan 4, 2013 at 6:58 PM, Foxchase jianming@gmail.com wrote:
Dear Henrik,
I'm trying aroma.affymetrix for Affy's Affymetrix Mouse
Hi,
The error message says: Failed to retrieve genome information for
this chip type: GenomeWideSNP_6
From your reply to my message in your other thread Problem with
AffymetrixCelSet cmd it looks like you are indeed missing annotation
files. (Currently you only have the cdf, which basically
Hi,
On Wed, May 16, 2012 at 9:05 PM, sean nj njs...@gmail.com wrote:
Hi,
I did get rid of the error message when I ran :
unf - TextUnitNamesFile$byChipType(chipType)
I got this done by loading the aroma.affymetrix package, in addition to
aroma.core.
But
Hi Michelle,
Yes: just replace
plotTracks(fit);
by
plotTracks(fit, chromosome=2);
Best,
Pierre
On Mon, May 7, 2012 at 11:48 PM, Michelle suyi...@gmail.com wrote:
Hi Henrik,
On this page http://aroma-project.org/vignettes/PairedPSCBS-lowlevel you
showed how to make whole genome plots of
Hi,
On Wed, Apr 18, 2012 at 3:05 PM, Sathish Periyasamy
sathish.periyas...@gmail.com wrote:
I am getting the following error segs - getSegments(fit); The error
output is as follows:
Please assist me in solving the following error.
regards
chromosome tcnId dhId tcnStart tcnEnd
Hi,
On Thu, Apr 5, 2012 at 10:17 AM, Frederic Foucault
frederic.fouca...@gmail.com wrote:
Hello,
I follow the setup of the vignette but failed again
setwd(c:/Users/foucault/Bioinformatic/acne/Test/)
library(aroma.affymetrix);
library(ACNE);
verbose - Arguments$getVerbose(-10,
What is your sessionInfo() ?
Perhaps you need to upgrade aroma.affymetrix instead, although I don't
see why you would get this core dump.
Pierre
On Mon, Nov 7, 2011 at 6:20 PM, Peter Kang h.peter.k...@gmail.com wrote:
I just upgraded to 2.14.0 (Mac OSX), and I'm getting a 'core dumped'
error
Hi Ivan,
On Tue, Oct 25, 2011 at 1:35 AM, Ivan Smirnov vanya...@gmail.com wrote:
Hi Henrik,
I am trying to run the script:
options(echo = FALSE,digits=4)
library(aroma.affymetrix)
verbose - Verbose(threshold=-8, timestamp=TRUE);
dataSet=Gupta_CC
chipType - GenomeWideSNP_6
cdf -
. Do you know how to extract the raw
intensity for each probe ?
On Aug 8, 5:48 pm, Pierre Neuvial pie...@stat.berkeley.edu wrote:
Hi,
The 'annotationData' directory should be directly in your working
directory, as explained in the page Setup: Location of annotation
data files:http://aroma
Hi,
The 'annotationData' directory should be directly in your working
directory, as explained in the page Setup: Location of annotation
data files:
http://aroma-project.org/node/66
In your case, you need to change the current directory to ~/experiment/ by
setwd(~/experiment/)
(or by starting
Hi Yaping,
The cdf file should not be in the working directory, but in a
chip-type-specific subdirectory of the 'annotationData' directory, as
explained in the page Setup: Location of annotation data files:
http://aroma-project.org/node/66
Please see this page for further info. In your example,
Hi Fong,
The standard way to do this within the Aroma framework is to use
*links* to the directories you need. The best way to do this depends
on your OS, but in general this can be done within R using the
function 'createLink' (from R.utils), e.g.:
createLink(target=~/Data/annotationData)
Hi Allab,
'fracB' in the Aroma world has the same meaning as 'BAF' in the
Illumina BeadStudio world, that is, as you say, the fraction of signal
coming from the B allele at a given SNP: yB/(yA+yB). So the short
answer is that there is no conversion needed from 'fracB' to 'BAF'.
[Side note: we
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: 28 November 2010 22:57
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] DNAcopy parameter
On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial
pie...@stat.berkeley.edu wrote:
Hi,
The parameters used
Hi Yan,
You're right: removing files manually from data folders generated by
aroma.* is not a good idea. This is can be done directly within R
using the methods provided by the package.
In your case, I think you were doing :
cbs - CbsModel(ds);
ce - ChromosomeExplorer(cbs);
process(ce,
Hi,
The parameters used are the default parameters of the 'segment'
function of the DNAcopy package. If you search for 'DNAcopy
parameters' on the Search forum box at http://aroma-project.org, you
will find this recent thread which gives an example of how these
parameters can be changed:
Hi,
On Wed, Nov 24, 2010 at 4:17 PM, Yan Jiao y.j...@ucl.ac.uk wrote:
Hi Henrik,
Another question about the result is : is there a way to map the copy number
to the gene ID automatically?
You mean retrieving a list of genes contained in each DNAcopy segment
? No, this is not implemented in
Hi Wero,
Dario is right, as explained in http://aroma-project.org/node/66.
Also, I would recommend not to manually add data in the installation
directories of R packages. When you upgrade to a new version of R,
your data will still be stuck in the installation directory of the old
version.
Hi,
On Tue, Aug 3, 2010 at 8:12 AM, Ajanthah Sangaralingam
a.sangaralin...@qmul.ac.uk wrote:
Thank you for the reply. I actually need to get the log2 copy number ratios
form the raw .cel files of a GenomeWideSNP6.0 array - I was using CRMA1 but
am now repeating the analysis using CRMA v2.
I
Hi,
Most probably you haven't put the required CDF file in the
corresponding annotationData/chipTypes/ directory.
Have you read the vignette http://aroma-project.org/node/38 ? This is
well explained there.
Also, similar versions of this question have been answered on this
list, see for example
Hi Viking,
Note that your question has nothing to do with aroma.* packages, so it
should not be posted on this list.
In this particular case, I think the function to use is Google search :)
http://www.google.com/search?q=combine+data+frame
Pierre
On Thu, Jul 15, 2010 at 10:52 AM, Liang Cheng
Salut Emilie,
On Thu, Jul 1, 2010 at 10:13 AM, EmilieT temilie...@gmail.com wrote:
Hello,
I am using your R framework with a set of Affymetrix SNP 6 data and I
have a problem with the extractDataFrame function.
The result is an incomplete matrix with row duplication.
sessionInfo()
R
Hi,
Could you please report the output of sessionInfo() and traceback(),
and post a complete code example ?
Pierre
On Tue, Jun 29, 2010 at 10:09 AM, Liang Cheng vikingch...@gmail.com wrote:
Hello everyone,
I meet this error when I try to read 10 CEL files by using AffymetrixCelSet:
the
)
ces - getChipEffectSet(plm)
exData - extractDataFrame(ces, units=NULL, addNames=TRUE)
write.table(exData,file=fileName.txt,row.names=FALSE)
thank you very much,
Liang
2010/7/1 Pierre Neuvial pie...@stat.berkeley.edu
Hi,
Could you please report the output of sessionInfo
Hi Seth,
On Thu, Feb 18, 2010 at 5:32 AM, seth redmond
seth.redm...@imperial.ac.uk wrote:
I seem to be having some trouble generating an average file for a chip
effects set. I'm following the CRMA2 vignette (skipping the fragment lengths
normalisation). The CES seems to be generated OK, but
Hi Mike,
Did you try to (g)unzip all your CEL files in
rawData/GSE15907/MoGene-1_0-st-v1 ?
I don't think that aroma.affymetrix can handle gzipped CEL files.
Also, please report your sessionInfo()
Best
Pierre.
On Thu, Jan 28, 2010 at 8:45 AM, mike dewar mikede...@gmail.com wrote:
Hi,
First
Hi Max !
Short reply: you can get this information from the NetAffx annotation
files. For example, for GenomeWideSNP_6, the mapping can be retrieved
from
http://www.affymetrix.com/Auth/analysis/downloads/na29/genotyping/GenomeWideSNP_6.na29.annot.csv.zip
The first two columns are the SNP id
Hi Anguraj,
[cc'ing the mailing list in case other people run into the same problem]
I can reproduce the error. Pasting the error message you got in the
search box of aroma.affymetrix's discussion page I found this thread
Hi Zaid,
Does your file satisfy the requirements detailed on the corresponding
help page ?
http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch
Pierre
On Wed, Dec 9, 2009 at 4:18 PM, zaid z...@genomedx.com wrote:
Hello,
I'm trying to create a custom CDF file
Hi Maria,
I think you should report this problem to the Bioconductor mailing
list instead, as it has to do with BioMart and GenomeGraphs, not with
aroma.*
Cheers
Pierre.
On Fri, Dec 4, 2009 at 5:14 AM, Maria Traka maria.tr...@bbsrc.ac.uk wrote:
I am running GenomeGraphs with my exon data and
Hi Wenhong,
Here is the Human Exon Array Analysis vignette:
http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis
It's listed with the other help pages:
http://groups.google.com/group/aroma-affymetrix/web
Best,
Pierre
On Fri, Nov 6, 2009 at 4:27 PM, Wenhong
Hi Carol,
On Mon, Oct 12, 2009 at 9:15 AM, cjb carol.b...@gmail.com wrote:
Hi all,
I am following along with the Gene 1.0 ST Vignette:
http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis
and with Henrik's August 7, 2007 aroma.affymetrix tutorial.
All goes well
, 6:56 am, Pierre Neuvial pie...@stat.berkeley.edu wrote:
Hi Marco,
In case you haven't solved your problem yet...
I think they should be the same if you have analyzed your data using
one of the CDF provided by Affymetrix, which is most likely.
What are you calling the affy annotation file
Hi Marco,
In case you haven't solved your problem yet...
I think they should be the same if you have analyzed your data using
one of the CDF provided by Affymetrix, which is most likely.
What are you calling the affy annotation file for the SNP6.0 ? What
CDF have you used ?
Best,
Pierre.
On
proceed as before and this reference array will be used to
calculate log-ratios and perform segmentation.
Cheers,
Pierre.
Thanks again!
David
On Aug 11, 9:22 am, Pierre Neuvial pie...@stat.berkeley.edu wrote:
Hi David,
Your code seems to be correct, but see remarks below.
On Fri, Jul
2.4) and you
have 1.0.0 ...
Cheers,
Mark
On 07/08/2009, at 7:23 AM, Pierre Neuvial wrote:
Hi,
I'm having trouble analyzing a set of 250K SNP arrays using the CRMAv2
code from http://groups.google.com/group/aroma-affymetrix/web/code-snippets
:
I've got an error at the summarization
Hi Suman,
You can also use writeRegions directly, as in:
writeRegions(cbs, chromosomes=22, verbose=verbose)
This won't generate the ChromosomeExplorer report as in the code in my
previous post, but it will create the .xls file with copy number
regions.
Cheers,
Pierre.
On Sat, Jul 25, 2009
Hi ZZ,
First, could you please sign with an explicit name (and possibly
affiliation) or write using an explicit email address ? I (we) think
that's the least that can be expected from someone asking for advice
from this group.
You'll find an answer to the second part of your question below.
On
Hi Myriam,
On Thu, Jun 4, 2009 at 4:38 AM, Myriam myriam.peyr...@ki.se wrote:
Hi,
I have done (and seems OK, no error message) the low level analysis of
the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
results in 50 samples.
However, I cannot get through the steps of
Hi Michael,
On Tue, May 5, 2009 at 2:01 PM, mbaudis mbau...@gmail.com wrote:
Dear all,
when plotting local copy number values after normalization/chip
effects etc., one has to load the CnChipEffectSet (e.g.:
cdf - getCdf(cesN)
gi - getGenomeInformation(cdf)
Is there a shortcut to load
Hi,
Thanks, that's fixed now.
Pierre.
On Sat, Apr 25, 2009 at 4:56 AM, mako ma.ko...@gmail.com wrote:
Hi, Henrik and members
At first, congratulations on 3 years anniversary!
I may find little mistake at following URL.
Hi,
On Thu, Feb 12, 2009 at 4:25 PM, wukong wukongsu...@gmail.com wrote:
I am wondering whether aroma-affymetrix can read in CEL files that are
scattered in several directories.
For example, the user may want to provide a text file specifying the
full paths of CEL files.
The reason is that
Hi,
I guess that if cesN is your chip-effect set (containing all 8
arrays), and if 1:4 are the normal samples you want to do
cesNN - extract(cesN, 1:4)
ceR - getAverageFile(cesNN, verbose=verbose)
and then use this reference as you did before. Does this help ?
Cheers,
Pierre.
On Tue, Jan
Hi,
I have followed the steps of the CRMAv2 vignette:
http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method
using aroma.affymetrix version 1.0.0 and I got the following warning:
plotAllelePairs(acc, array=array, what=input, xlim=xlim/3)
On Wed, Jan 14, 2009 at 11:56 AM, Pierre Neuvial
pie...@stat.berkeley.edu wrote:
Hi,
I have followed the steps of the CRMAv2 vignette:
http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method
using aroma.affymetrix version 1.0.0 and I got
Thanks Henrik, it worked.
Pierre
On Fri, Jan 9, 2009 at 10:14 PM, Henrik Bengtsson h...@stat.berkeley.edu
wrote:
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
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, B=3, tags=B=3)
but parameter B is still 1:
print(acc)
AllelicCrosstalkCalibration:
Hello Mike,
I'm not sure what your problem is but it would certainly be helpful if
you could post a complete code example, the corresponding output, and
your sessionInfo().
That said, there have been several posts on the list about related
problems, see e.g this one:
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