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 wrot
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 wh
Hi,
Could you also send a code example that generated this error ? From
what you sent there is no way to know what you did that generated this
error.
Best,
Pierre
On Fri, Jan 31, 2014 at 9:24 AM, wrote:
> Hello sir,
>
> i am getting following error. i am giving session info() and traceback
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 nor
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 wrote:
> Hello, this is my first time using aroma.affymetrix, and I'm having many
> troubles. I
paper for example,
> http://www.ncbi.nlm.nih.gov/pubmed/22522925).
>
> I'd be interested in hearing more of your thoughts against this. Do you
> have an idea of how much resolution is lost by smoothing?
>
> Emilie
>
>
>
> On Tuesday, December 3, 2013 5:26:38 PM UT
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
gt; and my location is
>>>> >
>>>> >
>>>> > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2
>>>> >
>>>> > i just creat new folder in annotation data with name ch
ng function
>
> Error: Failed to create AffymetrixCdfFile object. Could not locate an
> annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and
> with filename extension 'cdf'.
>> getwd()
> [1]
> "C:/Users/nwayyin/Documents/R/win-
Hi,
Please create a new thread (with a relevant subject line) instead of
replying to an unrelated one.
See below.
On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED wrote:
>
>
> Greeting ,
>
> iam a Phd student , i try implement aroma package but its not working with
> me , i don't know where i
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 wrote:
> Dear Henrik,
> I'm trying aroma.affymetrix for Affy's Affymetrix Mouse Diversity Genotyping
>
Hi Joshy,
In order to narrow down the problem it would be nice to have some
information about the output of your script.
First, can you add an 'str' instruction in your last loop, as below:
for( chr in 1:24)
{
units <- getUnitsOnChromosome(gi,chromosome=chr);
pos <- getPositions(
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 Mon, Jun 18, 2012 at 5:39 PM, NT_CMU wrote:
> Hi
>
> I am new to aroma.affymetrix. I am not sure why the command
> "AffymetrixCelSet$byName" is not working.
>
> cs <- AffymetrixCelSet$byName("test.CEL",chipType =
> "../../annotationData/chipTypes/GenomeWideSNP_6")
This will not work becau
Hi,
On Wed, May 16, 2012 at 9:05 PM, sean nj wrote:
>
> Hi,
>
> I did get rid of the error message when I ran :
>
> > unf <- TextUnitNamesFile$byChipType(chipType)
>
> I got this done by loading the aroma.affymetrix package, in addition to
> aroma.core.
>
> But now I
Hi Ying,
This is a question for the Bioconductor mailing list, because it had
to do with the affxparser package (and nothing to do with the aroma
framework). Can you post it there ?
Cheers,
Pierre
On Mon, May 7, 2012 at 10:07 PM, sean nj wrote:
> Hi guys,
>
> I tried to convert recent customCD
Hi Michelle,
Yes: just replace
plotTracks(fit);
by
plotTracks(fit, chromosome=2);
Best,
Pierre
On Mon, May 7, 2012 at 11:48 PM, Michelle wrote:
> Hi Henrik,
>
> On this page http://aroma-project.org/vignettes/PairedPSCBS-lowlevel you
> showed how to make whole genome plots of TCN, the
> de
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 tcnE
Hi Andy,
On Mon, Apr 16, 2012 at 4:15 AM, Andyusa wrote:
> HI All,
>
> It was my first time to use the aroma to run two pairs of samples vs
> controls, but it turn out failure (detail below). Could anyone give me some
> advices? Thanks. Andy
>
> library("aroma.affymetrix");
> verbose <- Arguments
Hi,
On Thu, Apr 5, 2012 at 10:17 AM, Frederic Foucault
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, timestamp=TRUE);
>>
(forgot to cc the list)
-- Forwarded message --
From: Pierre Neuvial
Date: Wed, Nov 16, 2011 at 10:16 PM
Subject: Re: [aroma.affymetrix] Processing multiple Affymetrix arrays
To: Anguraj Sadanandam
Hi Anguraj,
On Wed, Nov 16, 2011 at 4:13 PM, Anguraj Sadanandam
wrote
Hi wisekh6,
Although you don't give the code you used to process this data, from
what you report it looks like you initially processed your data set
using the "full" chip type. See below.
On Fri, Nov 11, 2011 at 7:22 AM, wisekh6 wrote:
> Dear all,
>
> After processing Affymetrix GenomeWide SNP
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 wrote:
> I just upgraded to 2.14.0 (Mac OSX), and I'm getting a 'core dumped'
> error when trying to access
Hi Ivan,
On Tue, Oct 25, 2011 at 1:35 AM, Ivan Smirnov 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 <- Affymetrix
Hi Qian,
I'm not sure what the warnings mean, but please see below for the error.
On Mon, Oct 17, 2011 at 4:19 PM, Qian wrote:
>
> Dear all,
> I just start learning aroma.affymetrix package for Affy SNP6.0
> analysis. I downloaded ugp,ufl,acs file from the link
> http://www.aroma-project.org/ch
work now. Do you know how to extract the raw
> intensity for each probe ?
>
> On Aug 8, 5:48 pm, Pierre Neuvial wrote:
>> Hi,
>>
>> The 'annotationData' directory should be directly in your working
>> directory, as explained in the page "Setup: Lo
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 startin
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")
c
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 d
-
> From: aroma-affymetrix@googlegroups.com
> [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
&
Hi,
On Wed, Nov 24, 2010 at 4:17 PM, Yan Jiao 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 aroma.*
You
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:
http:
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, chromo
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.
Spec
Hi Gene,
On Tue, Sep 7, 2010 at 4:38 PM, Gene wrote:
> I couldn't get any of the output methods to work to save my GLAD
> segmentation results (see output below). When I took a look at the
> auto-generated GLAD directory gladData/gsk,ACC,-XY,BPN,-XY,RMA,A
> +B,FLN,-XY/Mapping250K_Sty+Nsp, I saw
>
> Best,
> Matt
>
> On Wed, Sep 1, 2010 at 3:20 PM, Pierre Neuvial
> wrote:
>>
>> Hi Matt,
>>
>> You want to *update* the package, not *patch* it: the difference
>> between updates and patches is explained at
>> http://aroma-project.org/howto
Hi Matt,
You want to *update* the package, not *patch* it: the difference
between updates and patches is explained at
http://aroma-project.org/howtos/updateOrPatch.
So, to update aroma.affymetrix, do:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
as explained at h
Hi Gene Tastic,
On Mon, Aug 16, 2010 at 2:57 PM, Gene wrote:
> I'm getting the dreaded "Exception: Cannot fit target function to
> enzyme, because there are no (finite) data points that are unique to
> this enzyme" error, that has popped up a number of times on this board
> previously. However t
Hi gouxiongpapa/felixli77quick,
See below.
On Thu, Aug 5, 2010 at 9:33 AM, gouxiongpapa wrote:
> Hi there
>
> I wonder some one could kindly help me out from this:
>
> I am trying to process a data set of affy snp 250K sty, and I just
> copied the steps in the vignette file: Estimation of total
Hi,
On Tue, Aug 3, 2010 at 8:12 AM, Ajanthah Sangaralingam
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 am putting all of the d
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
Hi,
One comment below.
On Wed, Jul 7, 2010 at 11:15 PM, Pierre Neuvial
wrote:
> Hi Emilie,
>
> Sorry for taking such a long time to reply.
>
> You are right: there was a bug in
> AromaUnitSignalBinarySet.writeDataFrame causing the same data chunk to
> be written several tim
nteger
> Number of bytes per column: 1, 4
> Footer: 20100215 21:16:37
> CETAffymetrixGenomeWideSNP_6Henrik
>
> Bengtssonh...@aroma-project.orgGenomeWideSNP_6.cdf484489553223f3cd9141404b2a926a40cf47d6f1aGenomeWideSNP_6,Full.cdf4932917453fbe0f6e7c8a346105238a3f3d10d4ecGenomeWideSNP_6,Ful
Hi Fong,
On Tue, Jul 6, 2010 at 11:19 AM, Fong wrote:
> Hi,
>
> I've been trying to update my aroma affymetrix installation to the
> latest version and I was running the command,
>
> downloadPackagePatch("aroma.affymetrix")
>
> but I run into these errors.
>
> Failed to source: http://www.braju.c
Salut Emilie,
On Thu, Jul 1, 2010 at 10:13 AM, EmilieT 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 version 2.11.1 (2
gt; csQN <- process(qn, verbose=TRUE)
> plm <- RmaCnPlm(csQN, combineAlleles=TRUE, mergeStrands=TRUE)
> fit(plm, verbose=TRUE)
> ces <- getChipEffectSet(plm)
> exData <- extractDataFrame(ces, units=NULL, addNames=TRUE)
> write.table(exData,file="fileName.txt",row.
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 wrote:
> Hello everyone,
> I meet this error when I try to read 10 CEL files by using AffymetrixCelSet:
>
> the application has reques
Hi Davide,
On Wed, May 12, 2010 at 5:32 AM, Davide Cora' wrote:
> Dear all,
>
> we are writing this email regarding the usage of the R package AROMA
> on an Affymetrix SNPChip 6.0 platform.
>
> We are currently using the Aroma Affy package to analyze a
> snpCHIP Affy 6.0 dataset, following the in
Hi Seth,
On Thu, Feb 18, 2010 at 5:32 AM, seth redmond
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 getAverage returns '0'
> fo
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 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 wrote:
> Hi,
>
> First of all: apologie
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
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/13b5
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 wrote:
> Hello,
>
> I'm trying to create a custom CDF file from a flat 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 wrote:
> I am running GenomeGraphs with my exon data and i get the following
> e
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 wrote:
> H
Hi Carol,
On Mon, Oct 12, 2009 at 9:15 AM, cjb 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 until I tr
Best,
Pierre.
>
> thanks a lot for the help!
>
> Best Regards
>
> Marco
>
>
> On Sep 16, 6:56 am, Pierre Neuvial wrote:
>> Hi Marco,
>>
>> In case you haven't solved your problem yet...
>>
>> I think they should be the same if you ha
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.
O
Hi,
Try using getNames, e.g.
getNames(cesN)
Cheers,
Pierre.
On Fri, Sep 11, 2009 at 8:26 AM, mbaudis wrote:
>
> Dear all,
>
> how can I access a vector containing all array names used during
> processing?
>
> Also, can one run the segmentation not by chromosome, but by array (or
> specify
Hi Suresh,
The answer is no as CBS is just a segmentation method, not a
segmentation and calling method as GLAD is. So what you can compare
between the two is just the output of the segmentation.
FYI there is also a wrapper for HaarSeg (also segmentation only) in
aroma.affymetrix, in case you'd
controls
and define your GladModel as
glad <- GladModel(cesNListT, cesNListC) ## add all your favorite
options for GLAD here
This way cesNListC will be averaged to build a "reference array" Then
you can proceed as before and this reference array will be used to
calculate log-ratios and
Hi David,
Your code seems to be correct, but see remarks below.
On Fri, Jul 24, 2009 at 6:39 PM, David wrote:
>
> Hi, to everyone!
>
> I working with a set of 27 Cervican Cancer tumors using Affy 100k. I
> would like to get the log2 value for each SNP.
>
> I´m running the vignette (Everything ru
2.9.x (BioC 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.
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 step:
> plm <- RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
> fit(plm, verbose=log)
20090806 12
Hi Peng,
Can you report the output of sessionInfo() and post the complete code
you have run before you got these warnings ? It is hard (for me at
least) to figure out what happened if I don't know what you did and in
which environment.
Cheers,
Pierre.
On Tue, Aug 4, 2009 at 10:28 PM, Peng Yu w
2009 at 7:28 PM, Pierre Neuvial wrote:
> Hi Suman,
>
> I think the easiest way to get the segmentation results into a text
> file is to use the code at the bottom of the Total Copy Number
> analysis vignette:
>
> http://groups.google.com/group/aroma-affymetrix/web/tota
Hi Suman,
I think the easiest way to get the segmentation results into a text
file is to use the code at the bottom of the Total Copy Number
analysis vignette:
http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0
Specifically, if cesN is your CnChipEffectSet, you c
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.
O
Hi Michael,
On Tue, Jun 9, 2009 at 3:22 AM, mbaudis wrote:
>
> Dear all,
>
> how can one generate the segmentation file (& modify it's format)
> without plotting images via ChromosomeExplorer? I have written my own
> method, and don't need the wast of processing time and space. Also,
> this would
OK, I meant the other way round: the name of the folder should be
rawData/CLP/GenomeWideSNP_6
not
rawData/CLP/GenomeWideSNP_6.0
Best,
Pierre.
On Thu, Jun 4, 2009 at 6:36 AM, Pierre Neuvial wrote:
> Hi Myriam,
>
> On Thu, Jun 4, 2009 at 4:38 AM, Myriam wrote:
>>
>>
Hi Myriam,
On Thu, Jun 4, 2009 at 4:38 AM, Myriam 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 defining the CEL f
Hi David,
First, a remark: it seems you're using CRMA v1; I recommend that you
use CRMA v2 instead, see this vignette:
http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method
At the end of this vignette there is a paragraph explaining how to
Hi Jing,
You have probably already figured this out by yourself already now,
but extractDataFrame is what you are after. However it is meant to
extract data from *subsets* of units, not for all units at the same
time. Otherwise it is likely that you will run into memory problems.
One thing you ca
Hi,
Thanks, that's fixed now.
Pierre.
On Sat, Apr 25, 2009 at 4:56 AM, mako wrote:
>
> Hi, Henrik and members
>
> At first, congratulations on 3 years anniversary!
>
> I may find little mistake at following URL.
> http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-nu
Hi Michael,
On Tue, May 5, 2009 at 2:01 PM, mbaudis 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 the ce
options for UPD analysis, but none of
> those would plug in directly (at least to my knowledge).
>
> As said, any help is appreciated!
>
> Kind regards,
>
> Michael.
>
>
> On Feb 17, 10:24 pm, Pierre Neuvial wrote:
>> Hi Michael,
>>
>> I would be happ
Hi,
On Thu, Feb 12, 2009 at 4:25 PM, wukong 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 I want to proce
Hi Michael,
I would be happy to try to help you here, but as Henrik suggested it's
hard to answer without knowing what chip type you are using/planning
to use... Can you be more specific ?
Best,
Pierre.
On Tue, Feb 3, 2009 at 1:38 PM, Henrik Bengtsson wrote:
>
> Hi,
>
> there are no methods o
Hi,
I don't know what the problem is. I tried your recipe on the HapMap
250K_Nsp and everything went fine:
library("aroma.affymetrix")
log <- Arguments$getVerbose(-8, timestamp=TRUE)
cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
cs <- AffymetrixCelSet$byName("HapMap270,500K,CEU,testSet"
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,
Your code looks OK, and 27 samples should be enough for the robust
average to be a reliable estimate "reference sample".
I guess that these experiments controls, is that right ? Can you share
an example of output of GLAD (by ChromosomeExplorer) and maybe CNAT on
a chromosome where it detects
oes the job.
Cheers,
Pierre
On Wed, Jan 14, 2009 at 11:56 AM, Pierre Neuvial
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.affymet
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/
Thanks Henrik, it worked.
Pierre
On Fri, Jan 9, 2009 at 10:14 PM, Henrik Bengtsson
wrote:
>
> Hi.
>
> On Fri, Jan 9, 2009 at 6:22 PM, Pierre Neuvial
> wrote:
>>
>> Hi,
>>
>> I would like to perform allelic crosstalk calibration using the 3
>> c
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)
AllelicCrosstalkCalibrati
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:
http://groups.google.com/gr
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