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
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
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
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 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.
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
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 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,-
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,
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
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
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
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
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 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 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
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 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!
;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,
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
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
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
[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
[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
[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
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
[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
[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
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
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,
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, 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 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,
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.
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,
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 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 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.
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 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
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
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
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
Hi.
On Wed, Jun 23, 2010 at 11:04 AM, mortiz wrote:
> hi everyone,
>
> im trying to develop a function based on FragmentLengthNormalization,
> but when i try to execute my new function it gives me the next error
> message:
>
> Error in process.NormalRegions(normalReg, verbose = verbose) :
> atte
Opps, I missed that it was the Mapping250K_Snp chip type. That one
only got SNPs and no pure CN loci, so there has to be another
explanation than the one I provided. So, again a complete script will
help troubleshoot.
/Henrik
On Wed, Jun 23, 2010 at 2:01 PM, Henrik Bengtsson
wrote:
>
Hi Johan,
this certainly looks like a computational hiccup. I never seen it,
though I can imagine various ways how it could happen. Instead of
guessing, do you have a complete script that you did, you did you type
the commands on the command line one by one? You are saying you did
the analysis
ou
>
> 2010/6/23 Henrik Bengtsson
>>
>> On Wed, Jun 23, 2010 at 7:00 AM, Liang Cheng
>> wrote:
>> > Thank you, Henrik
>> >
>> > So there is no function from aroma package, which can deal with the
>> > "xx.cel"
>> >
ackage that process CEL files in
various ways.
/Henrik
>
> Viking
>
> 2010/6/22 Henrik Bengtsson
>>
>> Hi Viking,
>>
>> On Tue, Jun 22, 2010 at 6:28 PM, Viking wrote:
>> > I am new to aroma-project. I didn't find some materials to learn how
>>
Hi Viking,
On Tue, Jun 22, 2010 at 6:28 PM, Viking wrote:
> I am new to aroma-project. I didn't find some materials to learn how
> to do it.
>
> Can somebody please help me? Thanks a lot.
although you new here, please allow me to use a bit of sarcasm,
because then I can award you the price of 'P
Hi,
as explained in the CRMAv2 vignette you need to download several
annotation files in addition to the CDF file. The error is about a
missing Aroma cell sequence file (*.acs), which you can download from:
http://aroma-project.org/chipTypes/Mapping250K_Nsp-and-Mapping250K_Sty
/Henrik
On Tue,
Hi Mamum,
On Fri, Jun 18, 2010 at 12:25 PM, Mamun Rashid wrote:
>
> Hi everyone,
> I am analysing some affymetrix exon array data. I have been performing some
> Quality checking of the data. I have plotted the residulas from the plm fit
> of
> raw intensity data.
>
> I am using the core CDF fil
Hi.
On Mon, Jun 21, 2010 at 2:26 PM, Albyn wrote:
> Dear all,
>
> I am new to R and aroma.affymetrix both. I have 25 SNP6.0 Cel files
> and I have to find out LOH and UPD. I would like to use
> aroma.affymetrix could anybody suggest me if it is a good idea to use
> this package???
You can do lot
Hi,
something must have going wrong with your intermediate data results
while you tried to use those earlier and incorrect annotation data
files. I recommend that start from scratch by completely deleting:
probeData/Mcels,QN/GenomeWideSNP_6/
plmData/Mcels,QN,RMA,A+B/GenomeWideSNP_6/
and rerun y
fymetrix.com/community/forums/index.jspa]. You
may also want send a message to Affymetrix Support
[www.affymetrix.com/support/] - in my experience they are also very
responsive. I would point them also to the above NetAffx query
results.
It's worth getting this right once and for all. F
Hi.
On Mon, Jun 7, 2010 at 4:41 PM, k o wrote:
> Dear Usergrop.
>
> while proccessing data from the 5000k Sty array (but not the Nsp set),
> I receive the folleowing error:
>
>> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>> csC <- process(acc)
> Error in sort.list(pairsToBuild) :
>
ke to return to what I said in my first reply:
>>> It is hard to tell what is happening and even if something goes wrong
>>> - try to zoom out a bit so you see most of the data cloud when
>>> plotting the signals after ACC. It looks like the data is zoomed in
>>
Hi Jack.
On Mon, Jun 7, 2010 at 3:36 PM, Jack Yu wrote:
> Hello,
>
> I sent an e-mail earlier regarding errors in running the total copy
> number vignette, but please disregard that as it turns out it was just
> an issue with the annotation files. Sorry for the inconveniences.
Good. I've just s
t, Jun 5, 2010 at 4:54 PM, Henrik Bengtsson wrote:
> Hi Jack.
>
> On Fri, Jun 4, 2010 at 7:43 PM, Jack wrote:
>> Hi all,
>>
>> Let me preface this by saying I'm an introductory user when it comes
>> to R. I have a list of massive CEL files and I need to obtain th
rands, verbose=-10);
> footer <- readFooter(acs);
> footer$srcFile <- list(filename=getFilename(db), checksum=getChecksum(db));
> footer$createdBy <- list(name="Seth Redmond",
> email="seth.redm...@imperial.ac.uk");
> writeFooter(acs, footer);
Other that
Hi Jack.
On Fri, Jun 4, 2010 at 7:43 PM, Jack wrote:
> Hi all,
>
> Let me preface this by saying I'm an introductory user when it comes
> to R. I have a list of massive CEL files and I need to obtain the copy
> numbers from them. The error message I've encountered when using the
> vignette (http:
k. Please compare to
what you got when you did.
/Henrik
>
> Best Regards
>
> Robert
>
>
> On Jun 2, 6:47 pm, Henrik Bengtsson wrote:
>> Hi.
>>
>> On Wed, Jun 2, 2010 at 11:16 AM, Ivanek, Robert wrote:
>> > HI Henrik,
>>
>> > I wa
red to fit the range.
>>
>> And the summary produce the following
>> R> summary(ufl)
>> length length.02
>> Min. :-32768 Min. :-32768
>> 1st Qu.: 614 1st Qu.: 541
>> Median : 1146 Median : 997
>> Mean : 1601
Hi Steve,
technically aroma.affymetrix should be able to handle the
Cytogenetics_Array chip type. I have recently added more tests for
this chip type as part of aroma.affymetrix's redundancy and system
tests. This assures the technical support. The chip type has its own
page (we're moving away
Hi.
On Wed, May 26, 2010 at 3:24 PM, Ivanek, Robert wrote:
> Dear Sir or Madam,
>
> I would like to analyse the copy number variation data from Affymetrix
> Mouse Diversity Array. I have not found any information on your website
> about this particular array.
I have created page for this:
http:
Hi.
On Thu, May 27, 2010 at 6:17 PM, seth redmond
wrote:
> I've been working through the CRMAv2 vingette here:
> http://www.aroma-project.org/vignettes/CRMAv2
Have you been following it exactly, or have you done modifications?
It always helps to show the code you are doing.
> And though
Hi.
On Tue, May 18, 2010 at 5:39 AM, Tae-Hoon Chung wrote:
> Hi, All;
>
> I have a simple question: What's the best way of performing multiple
> processing jobs of the same platform (Affymetrix SNP chips)?
>
> My concerns are as follows: (1) Many of the jobs involving Affymetrix SNP
> chips may a
Hi all,
aroma.affymetrix and friends have been updated and is now being rolled
out to the CRAN servers. It is highly recommended to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This update follows the April releases of R v2.11.0 and Bioconductor
v2.6, whi
Hi.
On Sat, May 15, 2010 at 6:10 PM, Gabriele Zoppoli wrote:
> Hi,
>
> I'm new here, and I'm sorry if I'll post obvious questions. I looked
> throughout the newsgroup and on the aroma.affymetrix web page, but I
> couldn't find the answer from my question, so here it is:
>
> I'm trying to analyze
Hi.
On Fri, May 14, 2010 at 10:36 AM, Markus Leber wrote:
> Dear Henrik,
>
> thank you very much for your support.
> You are right. I am sorry that I didn't notice this problem.
> Step "Calibration for crosstalk between allele probe pairs" works without
> problems now.
>
> Unfortunately at the b
Hi.
On Wed, May 12, 2010 at 12:23 PM, Smaug72 wrote:
> Dear Henrik,
>
> thank you very much for your reply.
> Again I installed R and CRMA v2 on a new virtual machine (Suse 11.2),
> so that I can step back if necessary.
To get the terms correct; you installed the aroma.affymetrix package.
CRMAv2
Hi.
On Tue, May 11, 2010 at 2:42 PM, Smaug72 wrote:
> Dear Henrik Bengtsson,
>
> we would like to use the CRMA v2 for our work.
> Unfortunately we receive errors.
>
> First we use a Linux system (Suse 11.2).
> I installed R (version 2.11.0) without any problems.
> Af
On Tue, May 11, 2010 at 11:20 AM, Tae-Hoon Chung wrote:
> Hi;
>
> This is what I got:
>
>> dataSet <- "HapMap500K,Sty";
>> tags <- "ACC,-XY,BPN,-XY,RMA,A+B";
>> chipType <- "Mapping250K_Sty";
>> cdf <- AffymetrixCdfFile$byChipType(chipType);
>> cdfM <- getMonocellCdf(cdf);
>> ces <- CnChipEffectSe
> Traceback:
> 1: .Call("R_affx_get_cel_file", filename, readHeader, readIntensities,
> rea\
> dXY, readXY, readPixels, readStdvs, readOutliers, readMasked, indices,
> as.i\
> nteger(verbose), PACKAGE = "affxparser")
> 2: readCel(getPathname(this), indices
o(ces, verbose = verbose, ...)
> 7: findUnitsTodo.ProbeLevelModel(plm)
> 8: findUnitsTodo(plm)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> The
R.rsp_0.3.6 R.cache_0.3.0
> [10] R.filesets_0.8.0 digest_0.4.2 R.utils_1.4.0
> [13] R.oo_1.7.1 R.methodsS3_1.2.0
>
> I am using 64-bit R-2.10.1 on Mac OS x.
>
> TH
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
>
What does
print(sessionInfo());
report after doing library("aroma.affymetrix")?
/Henrik
On Mon, May 10, 2010 at 4:47 AM, Chung Tae-Hoon wrote:
> Hi, All;
>
>
>
> I was trying to process Affymetrix 250K Sty SNP Chip of HapMap project using
> CRMAv2 algorithm.
>
> I was following the vignette on
Hi,
before doing anything else, please provide what
print(sessionInfo())
reports.
/Henrik
On Wed, Apr 28, 2010 at 12:43 PM, Nolwenn Le Meur wrote:
> Hi everyone,
>
> I am trying to analyze pooling-based GWAS (I am used to expression
> data but new to the GWAS field) .
>
> I have 2 datasets fr
0), the different
>> > probes are all replicates). So a matrix with a row for each SNP and
>> > two columns (one for each sequence) (in the case of CN probes only one
>> > sequence and the other column could be NA).
>>
>> > thank you very much,
>>
>
ssume.
/Henrik
>
> Karl
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: Friday, April 23, 2010 7:44 AM
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] fail
way, and have hbInstall("aroma.affymetrix")
install some of the optional packages (including sfit), but if they
are not installed, 99.9% of aroma.affymetrix will still work.
Cheers,
/Henrik
>
> Karl
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.co
will use that as the default in
aroma.affymetrix.
>
> -kk
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
> Sent: Thursday, April 22, 2010 7:46 PM
> To: aroma-affymetrix
> S
Hi.
On Thu, Apr 22, 2010 at 9:26 PM, mike dewar wrote:
> Hi,
>
> I'm trying to normalize data generated by the immunological genome
> project (immgen.org). They have released raw data for 128 arrays and I
> would like to preprocess their data. I'm very new to this, so
> apologies for any obvious
Hi.
On Thu, Apr 22, 2010 at 11:13 PM, Karl Kornacker
wrote:
> The key function AllelicCrosstalkCalibration has "stealth dependencies" on
> additional packages (sfit and/or expectile) which are currently unavailable
> for R-2.11. When might updated versions of these packages for R-2.11 become
> av
Please report your sessionInfo(). /Henrik
On Wed, Apr 21, 2010 at 11:51 AM, elodie wrote:
> Hi,
>
> I try to use aroma.affymetrix for Human Exon chip with custom CDF. I
> tested several BrainArray custom CDF (refseq, ense, vegae). Before, I
> used convertCdf() to convert cdf in good format.
>
> W
Hi.
On Tue, Apr 20, 2010 at 10:16 AM, mortiz wrote:
> hi everyone,
>
> I need to read the sequences of the probes from the GWS6.0 chip and it
> has taken me more than 12 hours to do it only for 2 chromosomes. Im
> guessing im doing something wrong, because the basepairnormalization
> has to do t
Hi.
On Thu, Apr 15, 2010 at 10:56 AM, step...@mnemosyne.co.uk
wrote:
> Dear aroma users,
> I am trying to run gcrma across a collection of human breast cell line CEL
> files without success - code has worked in previous aroma versions, and is
> still contemporary with documented instructions at
>
GF-file, see their
>> README file for the updated HuGene annotation file.
>>
>> BTW, I really hope that Affymetrix (and you) will soon update the
>> annotation files for the SNP arrays to hg19, i.e. human genome build
>> 37.
>>
>> Best regards
>&g
yName ("affy-brain-dev", cdf = cdf) #
> produces cell set class object
> R>
> R> bc <- GcRmaBackgroundCorrection (cs)
> R> csB <- process (bc, verbose = -10) # as suggested by Henrik
> Bengtsson
> Background correcting data set...
> Computing probe affinit
Hi,
On Tue, Mar 30, 2010 at 4:58 PM, Louie wrote:
> Hi, and thanks for your reply.
>
> On 27 Mar, 16:36, Henrik Bengtsson wrote:
>>
>> It is not clear from your description what the problem is. What to do
>> you mean by "skewed toward deletions"? Do you
metrixCdfFile$byChipType ("MoEx-1_0-st-
> v1,fullR1,A20080718,MR") # taken from http://www.aroma-project.org/node/31
> R> cs <- AffymetrixCelSet$byName ("affy-brain-dev", cdf = cdf) #
> produces cell set class object
> R>
> R> bc <- GcRmaBackgrou
Hi,
in a few moments, I will update a few pages on the aroma.affymetrix
Google Group so that they point to the new website
http://www.aroma-project.org/. This may cause the aroma.affymetrix
mailing list/forum to go down, meaning if you try to post a message a
message will bounce back to you with
points is not centered
> about the zero line. We have exhaustively checked the wet lab QC and
> everything looks good.
>
> I appreciate you having a look at these figures. Please let me know
> if you can suggest some further analysis. I was even wondering about
> doing quantile n
Hi.
On Fri, Mar 26, 2010 at 9:17 PM, Louie van de Lagemaat
wrote:
> Hi Henrik et al,
>
> I have been reanalyzing an older dataset of Mapping500K (Nsp+Sty)
> arrays for CNVs using aroma, and this works in general really well.
> However, I have noticed that overall many individuals in this
> partic
ut the control spots:
>
> plotDensity(cs,col=rainbow(35),ylim=c(0,0.7))
> legend(0,0.7,legend= as.character(1:35),fill=rainbow(35))
> plotDensity(cs,col=rainbow(35),ylim=c(0,0.7),types="pm")
> legend(0,0.7,legend= as.character(1:35),fill=rainbow(35))
>
> Che
; v1",
> verbose = FALSE, overwrite = FALSE, subsetToUpdate = NULL,
> typesToUpdate = "pm", indicesNegativeControl = NULL, affinities
> = NULL,
> type = "fullmodel", opticalAdjust = TRUE, gsbAdjust = TRUE,
> gsbParameters = NULL, .depre
normalization
outputs.
Hope this helps
/Henrik
PS. It is possible to attached PNGs to emails to this list; you may
want to share your figures.
>
> Thanks again,
> Dick
>
> On Thu, Mar 25, 2010 at 8:26 AM, Henrik Bengtsson
> wrote:
>> Hi.
>>
>> On Th
Hi.
On Sun, Mar 14, 2010 at 3:04 AM, Yong wrote:
> Hi Everyone,
>
> I kind of remember that it is difficult or not correct to analyze
> multiple datasets based on different array design like hgu133plus2 and
> HuEx-1_0-st-v2. So, I am wondering whether it is OK to pool different
> experiments toge
Hi.
On Thu, Mar 25, 2010 at 5:30 AM, dbe...@u.washington.edu
wrote:
> Hello,
>
> I would like to get more info, perhaps example calls, on the various
> subclasses of ProbeLevelTransform.
>
> I see from a previous post by Mark Robinson, I have the examples:
> if(doNorm){
> bc <- RmaBackground
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