It sounds like on of your CEL files are corrupt. Start out with the 5
CEL files that work and add other CEL files one by one to the
directory to figure out which work and which do not. Also, the CEL
files should roughly be of the same file size; if one is much
different that is a likely clue that
Dear Viking,
please do not hijack old threads that are unrelated to your question.
It is like if a librarian would put books backs in random locations
making it hard for others.
On Fri, Jun 25, 2010 at 9:40 AM, Liang Cheng wrote:
> Hi Henrik,
> I read your file aroma.affymetrix :Analysis of smal
Please see FAQ. 2007-05-24 on http://aroma-project.org/FAQ
/Henrik
On Fri, Jun 25, 2010 at 10:49 AM, Liang Cheng wrote:
> Henrik,
> I found that if I want to read CEL files, I have to get the CDF files. Where
> can I get the ones mentioned in your slider, especially the 250k ones?
> thanks a lot
Hi Christian.
On Tue, Jun 29, 2010 at 3:39 PM, cstratowa
wrote:
> Dear Henrik,
>
> Until now I have used aroma.affymetrix_1.1.0 with R-2.8.1 and could
> run my analysis on our sge-cluster w/o any problems.
>
> Now I have upgraded to R-2.11.1 and to aroma.affymetrix_1.6.2 and are
> curently testin
Hi.
On Sat, Jul 3, 2010 at 2:22 AM, larryns wrote:
> Okay I managed to debug the problem. It seemed that indexOf didn't
> like my filenames because the files had parentheses in the name.
Your troubleshooting is correct, and yes, related issues have been
reported before;
Thread 'ArrayExplorer p
Hi Richard,
sorry for the delay - this one slipped through and I simply missed our
message, but I caught it while troubleshooting the same problem
reported in thread 'ArrayExplorer issue' started on 2010-07-02.
The reason for your problems is a bug in aroma.core/R.filesets that
causes hiccups whe
Hi Johan,
On Wed, Jun 30, 2010 at 9:13 AM, Johan Staaf wrote:
> Dear Henrik,
> I get an error when trying to extract CRMAv2 processed data when using the
> extract() function like below.
>
> cesSamples <- extract(cesNList[[chipType]], assay.vector)
>
> The error occurs when the assay vector conta
Hi,
before continuing, do you have the latest version of aroma.affymetrix
(v1.6.0) installed, e.g. what does
library("aroma.affymetrix");
print(sessionInfo());
report? You probably also want to update to R v2.11.1 (R v2.9.0 is rather old).
Second, the annoationData/ directory should be located
Hi.
On Fri, Jul 16, 2010 at 11:13 AM, Ajanthah Sangaralingam
wrote:
> Hi,
>
> I have been doing some paired total copy number analysis in aroma afyymetrix.
> The dataset I have is complicated for haf the dataset I have reference
> samples, for the other half I will do an unpiared analysis.
So,
Hi,
answer below.
On Fri, Jul 16, 2010 at 4:48 AM, biobee wrote:
> I am doing an upaired copy number analysis with 500K arrays using the
> CRMAv2. I want to use a subset of my samples the reference, instead of
> the all the samples as robust average for CBS segmentation.So I want
> to run CBS as
Hi Markus,
sorry but this one slipped through my net.
On Thu, Jun 17, 2010 at 5:27 PM, Smaug72 wrote:
> Dear Henrik,
>
> unfortunately we are faced with another problem.
> We processed several CEL files with CRMAv2 as decribed by vignette:
> http://aroma-project.org/vignettes/CRMAv2
> We receive
Hi, please ignore this message. I am trying to figure out why messages
that I have sent (group owner) yesterday have not been delivered to
the group and mailinglist archive. /Henrik
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to repo
Hi,
answer below.
On Fri, Jul 16, 2010 at 4:48 AM, biobee wrote:
> I am doing an upaired copy number analysis with 500K arrays using the
> CRMAv2. I want to use a subset of my samples the reference, instead of
> the all the samples as robust average for CBS segmentation.So I want
> to run CBS as
Hi Markus,
sorry but this one slipped through my net.
On Thu, Jun 17, 2010 at 5:27 PM, Smaug72 wrote:
> Dear Henrik,
>
> unfortunately we are faced with another problem.
> We processed several CEL files with CRMAv2 as decribed by vignette:
> http://aroma-project.org/vignettes/CRMAv2
> We receive
Hi Nicolas,
thanks for reporting this unwanted feature. I've fixed it so that the
default filename is *,total.txt and *,fracB.txt, respectively. Until
the next release is available, you can Install a patch as:
library("aroma.affymetrix");
downloadPackagePatch("aroma.core");
FYI, the writeDataF
[reposting; the forum has hiccups and does not put my replies in the
archives or deliver to everyone.]
Hi Nicolas,
thanks for reporting this unwanted feature. I've fixed it so that the
default filename is *,total.txt and *,fracB.txt, respectively. Until
the next release is available, you can In
[sorry for reposting; the forum does for some reason not deliver
messages sent from my main email account.]
Hi Nicolas,
thanks for reporting this unwanted feature. I've fixed it so that the
default filename is *,total.txt and *,fracB.txt, respectively. Until
the next release is available, you c
Hi Nicolas.
On Tue, Jul 20, 2010 at 11:42 AM, Nicolas Vergne
wrote:
> Hi everybody,
>
> I use ACNE for the normalization of SNP6.0 chip arrays.
> As ACNE is a multi-array methode, I would like to know if there is an
> option to precise the dataset of reference in the doACNE function?
You may ask
[reposting; still problems with the Google forum.]
Hi Nicolas.
On Tue, Jul 20, 2010 at 11:42 AM, Nicolas Vergne
wrote:
> Hi everybody,
>
> I use ACNE for the normalization of SNP6.0 chip arrays.
> As ACNE is a multi-array methode, I would like to know if there is an
> option to precise the datas
[2nd repost of this message - now from the Google Group web interface;
still problems with the Google forum.]
Hi Nicolas.
On Tue, Jul 20, 2010 at 11:42 AM, Nicolas Vergne
wrote:
> Hi everybody,
>
> I use ACNE for the normalization of SNP6.0 chip arrays.
> As ACNE is a multi-array methode, I woul
[sorry my repost did not contain my full reply due to a cut'n'paste
error.]
Hi Nicolas.
On Tue, Jul 20, 2010 at 11:42 AM, Nicolas Vergne
wrote:
> Hi everybody,
>
> I use ACNE for the normalization of SNP6.0 chip arrays.
> As ACNE is a multi-array methode, I would like to know if there is an
> op
to aroma.*.
/Henrik
>
> One other question:
> Is it allowed to delete the contents of directory .Rcache/
> aroma.affymetrix/idChecks?
Yes, it should be safe to delete any .Rcache/ as long as no R session
is in the process of writing to it. It's a cache containing redundant
to aroma.*.
/Henrik
>
> One other question:
> Is it allowed to delete the contents of directory .Rcache/
> aroma.affymetrix/idChecks?
Yes, it should be safe to delete any .Rcache/ as long as no R session
is in the process of writing to it. It's a cache containing redundan
Hi,
it's hard to say what causing this, but if you see it in several
samples at the same location, then my immediate thought is that you
reference signal may carry it. Are you using the average of the pool
of all samples as a reference or how do you calculate it? How many
samples to you have in
gt; > without a complete re-write of my package).
>>
>> Yes, I neither know of a functional mutex implementation in R. You
>> can achieve some by utilizing the lock mechanisms of data base servers
>> (not SqlLite), but nothing ready is available to my knowledge.
>>
Hi,
it's hard to say what causing this, but if you see it in several
samples at the same location, then my immediate thought is that you
reference signal may carry it. Are you using the average of the pool
of all samples as a reference or how do you calculate it? How many
samples to you have in
;Prostate/tmp", where these files are stored. In my case this would
> definitely solve my problem since each subdirectory would contain its
> own temporary directory, e.g. "Prostate/Prostate21/tmp". I do not know
> if this change would break any code or cause any problems, i
Hi all,
new versions of aroma.affymetrix and friends have been released. It
is highly recommended to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
In addition to some added features, there were also a few bugs fixed
in this release. Thanks for the reports!
time as Process A
writes, there is a potential problem.
>From my troubleshooting, as far as I understands it, the only way you
could have gotten that error message was when two or more processes
did getAverageFile(cesList[[1]]) where getNames(cesList[[1]]) where
identical. Are you 100% sure th
Hi Steven.
On Mon, Jul 26, 2010 at 9:00 PM, Steven Bosinger
wrote:
> Hi,
>
> I'm new to aroma and bioC in general, so these are probably a very
> straightforward questions:
>
> I am using aroma to get QC on some Human Affymetrix Gene arrays.
>
> 1. To keep it consistent with previous analyses usi
Hi Fong(?).
On Sat, Jul 24, 2010 at 2:10 AM, Fong wrote:
> Hi,
>
> I've used aroma.affymetrix to generate and extract the probeset
> summaries (chip effects) from a set of Human Exon array samples I
> have. And then performed batch adjustment on these probeset summaries
> using another R script
Hi Sundar,
I've been leaving your messages to the FIRMA experts, because they can
better answer you questions. However, I'll give a quick reply to the
things I can answer.
On Mon, Aug 2, 2010 at 6:59 PM, Sundar wrote:
> Hi,
> I am trying to analyze Mouse Exon 1.0 st array data using
> aro
Hi,
I'll leave the details to FIRMA experts, but you are using really
large values of argument 'ram'. It might be that you ran out of
memory (the you got an error message). If you used cut'n'paste,
instead of source(), to do the analysis, it might be that one of the
fit() methods was preemptivel
g/archive/GoogleGroups/web/caching.
This was a useful conversation to me; it made me see other ways for
(unnecessary) race conditions to occur, and remind me how important it
is to not overlook the smallest details in scientific communication
since they can make big differences.
Cheers,
Hen
M.chr <- log2(theta/thetaR);
> M.chr<-M.chr[uu,]
> check.chr.nbr[j]<-dim(M.chr)[1]
> # Save each chromosome at a time #
>
> save(M.chr,file=paste("CNdata/",data.set.name,"/chr_",j,"_",chipType,"_CopyNu
Hi,
you write:
annotationData/Chip type/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF
but that is *not* was is documented or written in the vignettes. You
should have:
annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF
It is really important that you use the correct directory names
wrote:
>>
>> HI but still I have a problem, These are steps i am doing
>>
>> 1. My current directory is on desktop where exactly my raw data is
>> 2. then I am trying to use the command in aroma.project
>> 3. I did changed the directory as you mentioned
>
Hi Gene,
did you add additional arrays to your rawData/ directory at anytime
after having ran the pipeline ones? If so, that would explain the
problem. The solution is then to delete the two plmData/
subdirectories:
plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/
plmData/gsk,ACC,-XY,BPN,-
mal analysis), I think Henrik gave all the
>> necessary information already, but
>>
>> assuming that 'idxT2' contains the indices of all tumor samples from a
>> particular tumor type in dsT that have a paired normal, and 'idxN2'
>> contains
Hi,
remove the temporary file GenomeWideSNP_6,Full,monocell.CDF.tmp in
annotationData/
chipTypes/GenomeWideSNP_6/ and retry. Be patient.
Note that, the first time you process a particular chip type/CDF (here
"GenomeWideSNP_6,Full"), a so called monocell CDF will be created.
This only happens onc
Hi Denis,
you refer to the thread 'Custom Canine SNP' started on July 18, 2008.
In KD's message on August 14, 2008 you can see how he explicitly set
argument genome="Canine" when he sets up the GLAD model. From the
verbose output I can see you are using CBS, but it is not clear how
you set it up.
6 0
> 20100823 11:06:14| Distribution of units with known fragment
> lengths and finite signals that are exclusively on this enzyme:
> Mode FALSE NA's
> logical 233566 0
> Error in list(`lapply(chipTypes, function(x) doCRMA("gsk", chipType
Hi,
if you are following Pierre's advice and still getting *that* error
message my best guess is that you are getting an error while
installing one of the packages that aroma.affymetrix depends on, which
in turn probably will fail the installation of aroma.affymetrix
itself. The reason why one of
Hi,
Q1. What is your sessionInfo() when the error occurs.
Q2. What is your working directories, i.e. what does print(getwd()) give?
/Henrik
On Fri, Sep 3, 2010 at 8:23 AM, AlexChen wrote:
> Hi,
>
> I want to use FIRMAGene package (http://bioinf.wehi.edu.au/folders/
> firmagene/sup3_04feb2010.R
rixStats_0.2.1
> [8] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3
> digest_0.4.2 GenomeGraphs_1.8.0 biomaRt_2.4.0
> FIRMAGene_0.9.5
> [15] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0
> loaded via a namespace (and not attached):
> [1] RCurl_1.4-3 too
mmy.txt");
>> cat(file=pathname, "Hello world!\n");
>> str(file.info(pathname));
> 'data.frame': 1 obs. of 7 variables:
> $ size : num 14
> $ isdir: logi FALSE
> $ mode :Class 'octmode' int 438
> $ mtime: POSIXct, format: "20
Hi.
On Fri, Sep 3, 2010 at 10:38 AM, Kai wrote:
> Hi everyone,
>
> Does anyone know whether the results from "multi-source copy-number
> normalization" can be further processed by segmentation model such as
> CBS and visualized in ChromosomeExplorer?
First of all, if it is possible to pass a CN
Hi Vonn.
On Fri, Sep 3, 2010 at 10:47 AM, Vonn wrote:
> Hi All,
>
> I'm interested in doing some basic quality control with Affy SNP6.0
> chips. In particular, I'd like to get summary statistics and plot
> densities of the intensity values for each array both before and after
> normalization (al
Hi.
I know that that error message is not very informative here, but you
get the error because (i) you are merging arrays from two different
chip types and (ii) there are no samples that have the same name (cf.
http://aroma-project.org/node/77) in two sets. That is, you have
> Chip type #1 of 2
Hi Leif.
I actually never had verified that one can do PCR fragment-length
normalization on the MOUSEDIVm520650 chip type. It turns out that the
current method/estimator/algorithm [1] does not support this chip
type.
The reason is as follows. The Affymetrix assay for this chip type
digests/frag
Hi.
On Fri, Sep 17, 2010 at 12:58 PM, Matt wrote:
> Hi Henrik,
>
> I am processing the data from the 270 HapMap samples on the SNP 6.0
> arrays using the CRMAv2 method. I wrote a script to follow the steps,
> minus the plotting, outlined on
>
> http://www.aroma-project.org/vignettes/CRMAv2
>
> I
Hi,
On Tue, Aug 24, 2010 at 3:01 AM, Denis wrote:
>
> Hi Henrik,
>
> Sorry for the delay, I had some difficulties in getting GLAD strated
> (including gsl ...).
> What should I else say than your the best and thank you very much for
> your help. I finally got it. I would like to provide you with
Hi Kai.
I am aware of the issue, and it is on the todo list to add argument
specify that you don't want ratios to be calculated. There is
currently a secret workaround for this that should not be read as an
official documented feature [that's a warning for users reading this
thread in the future]
Hi,
it has been brought to my attention that the Google Group site, which
provides our mailing list and its archive:
http://groups.google.com/group/aroma-affymetrix/topics/
is not accessible from/blocked by certain countries. Luckily there
are some alternatives by other services providing arc
Hi Dario,
Pierre Neuvial has kindly provided a more up-to-date vignette for
doing paired total copy number analysis. You find it at:
http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis
See if that helps
/Henrik
On Wed, Sep 22, 2010 at 5:05 PM, Dario Strbenac
wrote:
> Hello,
>
see from the file footer, more clear if we do:
> str(readFooter(ugp));
List of 5
$ createdOn: chr "20100215 19:24:13 CET"
$ platform : chr "Affymetrix"
$ chipType : chr "GenomeWideSNP_6,Full"
$ createdBy:List of 2
..$ fullname: chr "Henrik Bengtss
Hi,
On Fri, Sep 24, 2010 at 1:27 PM, Vonn wrote:
> Hi All,
>
> I'm using aroma to analyze CEL files from 141 SNP 6.0 arrays. I fit
> the quality assessment model as follows:
>
> plm = RmaPlm(csR)
> fit(plm, verbose = log)
> qam = QualityAssessmentModel(plm)
>
> Then I'd like to produce NUSE and
Hi,
first of all, for this chip type you need to specify:
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
Moreover, you cannot use the custom CDF in the
GcRmaBackgroundCorrection step, and have to do the follow workaround
illustrated in the below example:
library("aroma.affymetrix");
Hi.
On Mon, Sep 13, 2010 at 4:19 PM, Patrick wrote:
> Hi everyone,
> I'm using AROMA's implementation of the CRMA v2 method to get copy
> number estimates for cancer samples, and I'm getting a very unusual
> result. Many of the samples have a chromosome where AROMA has called
> primarily copy nu
g for alternatives that are accessible
from within China, and the above seem not to be. It would be great to
solve this, because the archive is very useful resource.
Thanks
Henrik
On Tue, Sep 21, 2010 at 9:32 PM, Henrik Bengtsson
wrote:
> Hi,
>
> it has been brought to my attention t
sely the internal/private getAM() method. The
CbsModel and likewise does not know about this layer and happily
receives log2 ratios regardless of what is stored on file.
Hope this helps
/Henrik
>
> Best,
> Kai
>
>
>
> On Sep 20, 1:06 pm, Henrik Bengtsson wrote:
>> Hi
Hi.
On Mon, Sep 27, 2010 at 4:51 PM, Kai wrote:
> Hi Henrik,
>
> I was wondering whether there is a way I can fine tune the behavior of
> CbsModel. Sometimes the default algorithm produces too many small
> fragments right next to each other without much separation in mean
> copy numbers. Is there
0.9.0
> [10] digest_0.4.2 R.cache_0.3.0 R.utils_1.5.2
> [13] R.oo_1.7.4 R.methodsS3_1.2.1
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
> The working directory is desktop and the path for the cdf file and the raw
> data is as f
hile, say. It could be a software/annotation bug
in the Affymetrix DAT to CEL file conversion and so on. That's why it
is crucial to know more about the chip used.
I also recommend that you try dChip and/or Affymetrix GTC, if possible.
/Henrik
> Thanks,
> Patrick
> On Sun, Sep 26, 201
say. It could be a software/annotation bug in the Affymetrix DAT to CEL file
> conversion and so on. That's why it is crucial to know more about the chip
> used.
>
> I also recommend that you try dChip and/or Affymetrix GTC, if possible.
Since it is GenomeWideSNP_6, you should
Hi.
On Tue, Sep 7, 2010 at 6:51 AM, wrote:
> Hi Henrik,
>
> Thanks for your response. Let me clarify what I'm trying to do: For each
> array I want to be able to compute basic summary statistics (min, median,
> max, etc.) of the probe-level intensities, both before and after
> normalization.
not detect this problem there. If NAs should be allowed, the fix
should be simple, but has to be done by me updating the code.
I'll get back to your when I've done this.
> Also I am getting some output in the probeData folder as:
> probeData/Exon Data,OBC/MoEx-1_0-st-v1/(all the *.cel fi
Hi.
On Wed, Sep 29, 2010 at 8:00 PM, Dario Strbenac
wrote:
> Hello,
>
> I remember reading a while ago that you can pass in additional parameters to
> CbsModel, and they will get passed onto DNAcopy functions. However, it
> doesn't seem to be working for me. I don't want any segments less than
Hi.
On Wed, Oct 13, 2010 at 5:24 PM, Yue Hu wrote:
> Hi,
>
> Just shift from affymetrix to agilent recently and since I prefer
> the plot generated by aroma.affymetrix I am just wondering if
> aroma.affymetrix is able to handle agilent chip data in some way.
When you say "plot generated by arom
Hi.
On Thu, Oct 14, 2010 at 4:38 AM, allab wrote:
> Dear aroma users/authors,
> i am doing now Affy 6.0 SNP data analysis and my goal is to become BAF
> values so that i can further use them with the method SOMATICS
> (Assie'08).
> I have not used from the very beginning the wrapper
> ds <- doASC
Thanks for follow up/reporting back to the list.
/Henrik
On Thu, Oct 14, 2010 at 12:03 PM, Fong wrote:
> For those interested I got a reply from the makers of the CDF files
> and apparently it is an issue on their end. Here is their reply:
>
> We have been studying the problem and we have disco
20100926.acs - Aroma Cell Sequence (ACS) annotation
file mapping cell indices to 25-mer sequences and target strandness.
Sources: Affymetrix probe_tab file. The latter provides only
4,779,314 (72.9%) out of 6,553,600 sequences; please help us find the
sequences for the remaining probes. Created by: He
ow can I send the results to be
> displayed by chromosome explorer?
>
> Thanks again for your help. I look forward to hearing from you soon.
>
> Best,
> Kai
>
>
>
> On Sep 27, 9:47 pm, Henrik Bengtsson
> wrote:
>> Hi.
>>
>> On Mon, Sep 27
; process(ce,chromosomes=c(1:23),min.width=5);
>>
>> I am not clear where I should put "min.width=5"? If I do
>> "process(cbs,min.width=5)" first, how can I send the results to be
>> displayed by chromosome explorer?
>>
>> Thanks again for yo
tRegions(cbs)[[4]][139,1:5]
> chromosome start stop mean count
> 139 16 45057510 45057696 -1.427 2
>
> It seems to me that min.width=5 worked only in the first sample. Do
> you have any idea on this? Thanks!
>
> Best,
> Kai
>
>
> On Oct 26,
Hi.
On Wed, Nov 3, 2010 at 6:03 AM, Oscar Rueda wrote:
> Hi all,
>
> I'm trying to normalize several thousands of tumor samples using aroma. The
> BAF profiles I get using
>
>> AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=FALSE)
>
> are quite noisy, so I have started using ACNE for getting 'c
Hi there,
thanks all for citing our publication directly or indirectly related
to the aroma project framework.
Since I noticed that the original CRMA paper often get cited even when
the CRMA v2 method is used/meant, I would like to clarify to the list
that CRMA v2 is preferably referenced as:
H.
Hi.
On Thu, Nov 4, 2010 at 3:11 AM, Oscar Rueda wrote:
> Hi Henrik,
> Many thanks for your detailed response even when I didn’t include some
> important information.
>
> See comments below.
>
> On 3/11/10 23:00, "Henrik Bengtsson" wrote:
>
> Hi.
>
>
Hi.
On Fri, Nov 5, 2010 at 9:09 AM, Hans-Ulrich
wrote:
> Hi all,
>
> I am using the Affymetrix "MOUSEDIVm520650" chip. During the the
> normalization step for fragment length, the aroma software complains
> that no probes for enzyme 1 only exist (the same for enzyme 2). I
> found
> this discussio
Hi all,
aroma.affymetrix v1.8.0 and friends have been released and is being
rolled out on CRAN as we speak. It is highly recommended to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This update follows the September releases of R v2.12.0 and
Bioconductor v
name);
Also, have a look at thread 'Custom Canine SNP (DogSty06m520431);
problem with chr24-39 Options' started on August 23, 2010:
https://groups.google.com/group/aroma-affymetrix/browse_thread/thread/9593afed0d424450/d4e9de835c224db8
Hope this helps
Henrik
>
> Best wish
More below...
On Tue, Nov 9, 2010 at 1:16 PM, Henrik Bengtsson
wrote:
> Hi.
>
> On Tue, Nov 9, 2010 at 3:37 AM, Hans-Ulrich
> wrote:
>> Hi Henrik,
>>
>> thank you very much for your help! I tried your code and it seemed
>> that I got reasonable result
Hi,
the fileAccess() write-permission test actually tries to write a small
file to the directory to assert you have write permission to it. It
seems like it cannot create a file and write to it in that directory.
That provides an additional test on top of what file.access() does.
(The filename 'K
Hi,
thanks for reporting this. Unfortunately, the R-forge site is lagging
behind in providing builds etc. I'll report to them, since this is
beyond my control. In the meanwhile, see if the following works for
you
source("http://www.braju.com/R/hbLite.R";);
installPackages("http://www.braju.com
got R.utils
1.5.6. Using that code had no affect on your issue.
> But then i came across a Disk quota exceeded, which i guess is upto
> the sys admin to fix...
So that was the real cause.
Thanks for reporting back.
/Henrik
>
> Thanks again..
>
> Regards
> Elsa
>
aR), e.g. the robust average of all arrays, e.g. C = 2
* theta / thetaR. This is, by definition, not an issue for BAF.
That you get some negative values is not strange either, because they
may occur after subtracting offset ("background") in the signals.
Think about them as noise around z
Hi,
if you tried to update to aroma.affymetrix v1.8.0 but you're still
stuck with v1.7.0, then it was due to a server mistake. It should
work now:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Sorry about that!
/Henrik
--
When reporting problems on aroma.affyme
Hi,
the Aroma Project *web site* will be down for maintenance tomorrow
Saturday November 14, 2010. It is expected to start at 06:00 UTC
(midnight EST) and last no longer than 14:00 UTC (8am EST).
The mailing list will NOT be affected, that is, you can still post
questions to the list.
/Henrik
Hi.
On Mon, Nov 15, 2010 at 8:50 PM, Elsa Chacko wrote:
> Hi
>
> I am trying to implement the Vignette: Human exon array analysis
> posted at http://www.aroma-project.org/node/37.
>
> However when i got to the section discussing how to browse spatial
> false-colored images of the residuals,
>
> a
R-FORGE
> INCLUDES THE REAL EBIMAGE PACKAGE OR SETS
> R_check_force_suggests=false.
>
> Seeing the aroma.affymetrix in the message i wrongly assumed that this
> is an error message from the aroma package..
>
> Thanks for the assistance
> Regards
> Elsa
>
> On Nov 1
t;EBImage") -
you should get an error.
Then restart R, and try to install from Bioconductor.
/Henrik
> But again as mentioned it could be due to the version of R. we are
> trying to get R updated and will see how things go from there.
>
> Thanks for the assistance
> Regards
>
Hi,
I suspect that you have an incomplete CDF file, e.g. due to
downloading errors. Verify that you get the same output as the
following:
> print(cdf);
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
Filesize: 176.32MB
Chip type:
Hi.
On Thu, Nov 18, 2010 at 9:40 AM, Yan Jiao wrote:
>
> Dear all,
>
> I’m trying to solve my copynumber segmentation problem using aroma
> affymetrix, according to the Vignette
>
> I created a folder : rawData ,under my working directory, and inside that
> folder I created another folder Mappin
Hi again,
On Fri, Nov 19, 2010 at 10:35 AM, Henrik Bengtsson
wrote:
> Hi.
>
> On Thu, Nov 18, 2010 at 9:40 AM, Yan Jiao wrote:
>>
>> Dear all,
>>
>> I’m trying to solve my copynumber segmentation problem using aroma
>> affymetrix, according to the Vign
Hi,
I don't know what system you have but a rough estimate is 3-10 minutes
per array, which then is 1800-6000 minutes or 30-100 hours or 1.25-4.2
days for 600 arrays. It's not mega fast but it is also not that slow,
especially not when you compare how long it takes to run the assay for
600 arrays
Hi.
On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao wrote:
>
>
> Dear all,
>
> I’m trying to do DNA segmentation,
>
> This is what I’m doing:
>
> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", verbose=TRUE);
>
> ###this is done sucessfully
>
> # Segmentation
>
> cbs <- CbsModel(ds);
>
>
>
Unfortunately, it
does not work for the 64-bit version of R on Windows 64-bit. It works
if you do tricks an run the 32-bit version of R, but that is a rather
inconvenient workaround.
/Henrik
>
>
> Yan
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailt
t not found. Searched directories: C:/gs, C:\Program Files/gs,
> /gs, C:\Program Files\Common Files/gs
>
> Are those warning messages serious? Could I ignore them?
>
>
> Yan
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affy
where the error occurs.
/Henrik
>
>
> Many thanks
>
> yan
>
>
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 15:08
> To: aroma-affymetr
7 72
>
> Sample names:
>
> [1] "GSM255038" "GSM255039" "GSM255040"
>
> Full sample names:
>
> [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>
> Compiling RSP...done
>
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