Hi,
aroma.affymetrix v2.7.0 is available. As usual, it is highly
recommended to update, which you can do by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This release consists of several updates throughout the suite of
aroma.* and R.* packages. As alw
Hi,
first thing to try whenever running out of memory in R is to retry in
a fresh R session. That often solves the problem. It's also useful
to know that all your aroma analysis is automatically stored on your
file system, so when you restart aroma will quickly skip the step you
did before.
If
the same as:
units <- findUnitsTodo(plm);
str(units);
## int [1:934968] 622 623 624 625 626 627 628 629 630 631 ...
If so, the try with
units2 <- fit(plm, verbose=-10);
and compare to the output I already pasted in my previous message (below).
/Henrik
>
>
> On Monday, 26 Novemb
Hmm... first run this in a fresh R session:
library("aroma.affymetrix");
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
csR <- AffymetrixCelSet$byName("test", cdf=cdf);
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2");
csC <- process(acc, verbose=verbose);
bpn <- BaseP
here
> str(units)
> }
>
> 3. > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.
Hi,
please provide the following information so I can help troubleshoot:
1. What's your sessionInfo() after doing library("aroma.affymetrix")?
2. Your complete script (right now I not sure which chip type your are
working on) up to the point where you get the error.
3. The output of print(cdf)
On Thu, Nov 22, 2012 at 6:35 AM, Raj Patrao wrote:
> Hello Henrik, thanks for the reply.
>
> the tmp folder is within the GSE4757,GRBC folder, which is not getting
> renamed (throwing error).
Which tmp folder, what's the error message and in what step is this created?
/Henrik
>
> -Rajesh
>
>
>
On Mon, Nov 19, 2012 at 8:53 PM, Raj Patrao wrote:
> Hentrik,
>
> I did delete all the files created and re-ran. I deleted complete folder
> structure below , as these files are created automatically .
>
> probeData
> GSE4757,GRBC
> GSE4757,OBC
Are you saying things work now?
>
>
> Als
CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.aff
Hi,
I've never seen that before, but remove any *.tmp or *.tmp.tmp etc
files and try again. If that does not work, then please
1. show your script exactly at it is,
2. show the output you get from
library(aroma.affymetrix);
sessionInfo();
/Henrik.
On Sun, Nov 18, 2012 at 8:02 PM, Raj Pat
Hi,
this is a question for the Bioconductor mailing list - please repost there.
/Henrik
On Sun, Nov 11, 2012 at 5:16 AM, Svetlana Vinogradova wrote:
> My question is the following:
>
> I have Affymetrix SNP 6.0 chip data loaded in R as ExpressionSet object:
>
> ExpressionSet (storageMode: locke
Generic support for retrieving probe sequence data from Affymetrix
probe tab files is a bit so and so, because it's hard for the code to
be agile to modifications of the file format that Affymetrix does over
time. Instead, try to add the ACS (Aroma Cell Sequence) file from:
http://www.aroma-pro
Hi,
sorry about that - a hiccup of mine (I've been slowly pushing updates via
the aroma server and am now pushing them to CRAN and I missed a bit here).
Retry with:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
and it should work.
/Henrik
On Thu, Oct 25, 2012 at
Hi,
thanks for reporting and sorry about this - a hiccup of mine (I've
been slowly pushing updates via the aroma server and am now pushing
them to CRAN). Retry with:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
and it should work. If not, please let me know.
/H
Hi,
more comments below.
On Fri, Oct 19, 2012 at 3:37 AM, Laurent Malvert wrote:
> from: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
>> On Thu, Oct 18, 2012 at 5:50 AM, Laurent Malvert wrote:
>>> [...]
>
Hi.
On Thu, Oct 18, 2012 at 5:50 AM, Laurent Malvert wrote:
> Hello Henrik and Aroma Affymetrix users,
>
>
> I understand you have been in contact with Jay over the integration of
> ArrayExplorer within our products, since the last time I wrote to you.
> He reported to me some issues with IE9,
Hi,
your CDF is most likely corrupt. You didn't tell us what
cdf <- AffymetrixCdfFile$byChipType("HTHGU133A_Hs_ENTREZG");
print(cdf);
outputs, and also not how you obtained that CDF. However, it looks
like (it originates from) a custom CDF by the BrainArray project
[http://brainarray.mbni.med.u
e skipped
more or less instantaneously.
/Henrik
>
>
> Thank you very much for your patience!
>
>
> Martina
>
>
>
> Il giorno lunedì 24 settembre 2012 19:55:51 UTC+2, Henrik Bengtsson ha
> scritto:
>>
>> On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen
Hi, sorry about the affxparser mess.
See if the following
source("http://aroma-project.org/affxparser.R";);
installAffxparser();
solves your problems. The above will run tests to make sure
everything works fine and if it says that is the case, you're read to
rock'n'roll.
Please report back and
Hi,
sorry, there is currently nothing in aroma.affymetrix for calling
probes present/absent. For questions on affy::mas5calls(), check with
the Bioconductor mailing list.
Cheers,
Henrik
On Tue, Sep 25, 2012 at 4:05 PM, Heather Wick wrote:
> I would like to look at present/absent calls and the
On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen
wrote:
> Hi,
>
> Last week I ran CRMA (v2): Paired total copy number analysis
>
> Using the following annotation files
>
> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
>
> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
>
> GenomeWideSNP_6,
Hi.
On Wed, Sep 19, 2012 at 5:36 AM, S. A. Haider wrote:
> Hi Guys,
>
> Following preprocessing (doCRMAv2), i am running segmentation using CBS. I
> have few hundreds of samples (~600 SNP6) and as far as i understand, aroma
> tries to keep memory usage to minimum. So far, it looks that it will ta
LRR are basically log2 CN ratios centered around 0 whereas CT are
non-logged CN ratios centered around 2 (or whatever you think the
ploidy is), so CT = 2^LRR should do.
/H
On Tue, Sep 18, 2012 at 6:28 AM, Reed wrote:
> I am trying to run segmentByPairedPSCBS on my illumina 1M dataset. This R
> f
HI, you need to give us way more information in order to help. Right
now your question is like "My car used to run well but not any longer
- what's wrong with it?"
FYI, we run extensive redundancy tests for each update to make sure we
are not breaking anything, so most likely you're not experienc
rop non-polymorphic ("CN") loci that
have same locations as other SNPs/CN loci. In the end of the day it won't
matter much what you do, because this only affects a teeny fraction of the
data you have.
/Henrik
>> Thanks,
>> Mike
>>
>> On Friday, Septe
On Fri, Sep 14, 2012 at 1:57 PM, Mike wrote:
> I am using aroma.affymetrix for pre-processing of data for CNV analysis.
> Briefly, I normalize and estimate copy number with CRMAv2. I use the
> calculated copy number along with the chromosomal locations from the ugp
> file to run CBS using segment
> position.
Yes, nothing in the TumorBoost method makes use of genomic locations
(nor chromosome or position); it normalizes tumor BAFs given the
corresponding matched normal BAFs for SNPs independently of each
other.
/H
>
> Reed.
>
> On Thursday, September 13, 2012 9:36:34 PM
memory in, say, a data frame and then pass those values to
normalizeTumorBoost().
/Henrik
>
> Please help.
>
> Reed
>
>
> On Wednesday, September 12, 2012 8:14:21 PM UTC+5:30, Henrik Bengtsson
> wrote:
>>
>> Hi,
>>
>> On Sun, Sep 9, 2012 at 10:18 PM,
Hi.
On Wed, Sep 12, 2012 at 6:07 AM, Maria Rodrigo wrote:
> Hi,
>
> I have come across an error when extracting probe intensities from the exon
> array using function getUnitIntensities()
>
> "Error in readCelUnits(pathnames, cdf = cdfUnits, readStdvs = FALSE,
> readPixels = FALSE, :
> No CDF
Hi,
On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap wrote:
> Hello,
>
> I have a question regarding to TumorBoost.
> I have data from Affymetrix (GenomeWideSNP_6) and Illumina (Omni1-Quad) for
> the same set of samples.
> I want to do normalization of CNV for the data from both platforms
> for t
Hi,
aroma.affymetrix v2.6.0 is available. Update by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This release consists mostly of internal framework improvements and
only a few minor updates for the end user, e.g. improvement of the
bpmapCluster2Cdf()
R solved my installation problems.
>
> Thanks,
> Mike
>
>
> On Thursday, September 6, 2012 2:31:52 PM UTC-4, Mike wrote:
>>
>> Thanks Henrik. I'll post back once I upgrade to let the community know
>> whether this solved my issues or not.
>>
>> O
On Thu, Sep 6, 2012 at 10:09 AM, Mike wrote:
> I am trying to install in R.12.1. Is this causing the problem?
That's certainly possible, yes. Although I try not to restrict the
code/packages to require the very latest versions of R, I do *not*
validate that they actually work for such old versi
file or nothing at
all. Thus, there is no risk of getting an incomplete download, which
you may indeed get if you use utils::download.file(). This is done by
first downloading to a temporary file, which is only renamed when the
download is complete. Just as most modern downloader are doing, e.g.
uEx-1_0-st-v2,coreR3,A20071112,EP.cdf";);
/Henrik
On Wed, Aug 29, 2012 at 11:52 AM, Henrik Bengtsson
wrote:
> Ok, there is something wrong with your downloads. Downloading that URL
> should give you a file that is exactly 40,108,891 bytes. Your
> downloaded file is of a different size
On Wed, Aug 29, 2012 at 6:38 AM, Jay wrote:
>
> Hi Henrik,
>
> Hope you are doing good. Firstly, thank you very much for your reply.
>
> I am extremely sorry for not attaching the screenshot. I am attaching it now.
> Please do let me know if you have any issue viewing this jpeg.
>
> Many thanks f
536
>> getFileSize(cdf)
> [1] 40119256
>> getChecksum(cdf)
> [1] "4edf1818f913069ba314e1358fc232a5"
>> packageDescription("affxparser")
> Package: affxparser
> Version: 1.28.1
> Date: 2012-03-30
> Title: Affymetrix File Parsing SDK
> Author: Henrik Ben
a/chipTypes/HuEx-1_0-st-v2
> ## Filename: HuEx-1_0-st-v2,core,A20071112,EP.cdf
> ## Filesize: 38.25MB
> ## Chip type: HuEx-1_0-st-v2,core,A20071112,EP
>
> ## RAM: 0.00MB
> ## File format: v4 (binary; XDA)
> ## Dimension: 2560x2560
> ## Number of cells: 6553600
> ## Number of uni
Hi,
it could be either a bad array or corrupt annotation files. I don't
know which UFL annotation data file you are using, but I recommend
that you download the most recent one from
http://aroma-project.org/data/annotationData/chipTypes/Mapping50K_Hind240/
and then confirm that you get:
> li
Hi,
On Mon, Aug 13, 2012 at 4:48 AM, Jay wrote:
> Thanks a lot for your reply. I managed to install successfully and its
> working only in firefox. I am using Firefox v13.0.1. Unfortunately I need to
> make this work in Internet Explorer 7 or 8. I am getting few javascript
> error. Please see the
Hi,
I see nothing wrong with your script. I suspect that the CDF you've
downloaded got corrupted or something. Do you get the same output as
below:
> library("aroma.affymetrix")
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags = "coreR3,A20071112,EP");
> cdf
## AffymetrixCdfFile:
## Path: a
Hi,
I'm not sure what is going on. It should certainly not get stuck for
14 hours, unless you're running out of RAM and you're swapping like
crazy, but that should not happen if you have, say, at least 1GB of
RAM. Are you doing this in a fresh R session?
Where it seems to hang has nothing to do
On Wed, Aug 1, 2012 at 11:31 AM, Fong wrote:
> Hi,
>
> I seem to be unable to figure out whether this question has been addressed
> or not so I apologize if this has already been asked. Basically I have a
> set of U133 arrays which I have processed through aroma.affymetrix and now I
> am just usi
Just a mistake. Thanks for spotting it. /Henrik
On Mon, Jul 23, 2012 at 4:36 PM, complexkid wrote:
> Hi Henrik,
> I just noticed your response in the thread :
> https://groups.google.com/forum/#!msg/aroma-affymetrix/RCHLDIfO47s/SJafAcaQnZsJ.
> Why is the following operation done twice ?
>
>
> htt
Before anything else, can you verify that your CDF is correct?
Confirm that you get the following:
> library("aroma.affymetrix");
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6
Hi.
On Wed, Jul 11, 2012 at 9:59 AM, Nir wrote:
> HI All,
>
>
> I am trying to run the standard procedures for a HuGene-1_0-st-v1 array.
>
> Here is the code:
>
> ---
>
> setwd("");
>
> library(aroma.affymetrix)
>
> chipType <- "HuGene-1_0-st-v1
This is most likely unrelated to the aroma framework and more likely
to be related to a setup issue with one of your PNG device drivers.
To troubleshoot, what does the following output give if you start a
fresh R session:
library("aroma.core");
pngDev <- findPngDevice(transparent=FALSE, force=TRUE
On Sat, Jun 30, 2012 at 11:41 PM, joshy wrote:
> Hi,
>
> Can anyone let me know where I can download the annotation files for this
> chipType CytoScan750K_Array
Didn't know of this chip; I've added
http://aroma-project.org/chipTypes/CytoScan750K_Array, where you find
a link to the Affymetrix prod
8.ufl"
"GenomeWideSNP_6,na31,hg19,HB20110328.ugp"
"GenomeWideSNP_6,HB20080710.acs" is the same for both CDFs.
/Henrik
>
>
>
> On Tuesday, June 26, 2012 11:51:49 PM UTC-4, Henrik Bengtsson wrote:
>>
>> Following the troubleshooting of annotationDat
Following the troubleshooting of annotationData/ on
http://aroma-project.org/troubleshooting/DirectoryStructures using
chipType <- "GenomeWideSNP_6", what does print(list.files(path=path))
output?
/Henrik
On Tue, Jun 26, 2012 at 8:04 PM, Andrew wrote:
> I feel it might be better to post my quest
Before anything else, you need to have matched tumor-normal pairs in
order to apply the TumorBoost method. No exceptions. So, at best, if
the 2 normals are matched with 2 of the tumors, you can can run
TumorBoost on those 2 pairs. Is that what you have?
/Henrik
On Mon, Jun 25, 2012 at 10:15 AM
Hi "hanat T",
I've looked at this and chatted with Mark Robinson about it and this
turns out to be a bug in bpmapCluster2Cdf(); it tries to exclude
non-genomic control sequences and it turns out it is too conservative
in what it calls a control sequence (cf. http://goo.gl/cjGnZ). This
bug had no/
o that) is working
with M = log2(T/N), which on the non-log scale is 2^M = T/N.
/H
>
> Thanks,
> Michelle
>
>
>
> On Fri, Feb 17, 2012 at 6:04 PM, Henrik Bengtsson
> wrote:
>>
>> Hi,
>>
>> On Fri, Feb 17, 2012 at 1:44 PM, Michelle wrote:
>> &
You can ignore them. Warnings are almost always alright - errors are not.
/Henrik
On Tue, Jun 19, 2012 at 6:40 AM, NT_CMU wrote:
> Thank you Henrik and Pierre. I am able to run it successfully now.
>
> It gives me a few warnings at the end.
>
>> warnings()
> Warning messages:
> 1: In log2(y) :
Hi,
you should also get the following annotation files:
annotationData/
chipTypes/
GenomeWideSNP_6/
GenomeWideSNP_6,Full,*.acs
GenomeWideSNP_6,Full,*.ugp
GenomeWideSNP_6,Full,*.ufl
as explained in for instance
http://aroma-project.org/vignettes/CRMAv2. You can get them from
http:/
On Mon, Jun 18, 2012 at 1:59 PM, NT_CMU wrote:
> Hi
>
> Thanks for the help Pierre. I managed to resolve it. I am just using the
> AffymetrixCelSet$byName with the cdf information instead of the chipType.
> For some reason, that still refuses to work.
These are the two possible ways to setup the
milar
conversions have done before so everything "should be ok".
/Henrik
On Wed, Jun 13, 2012 at 5:24 PM, Henrik Bengtsson
wrote:
> Hi.
>
> On Tue, Jun 12, 2012 at 1:17 AM, dave wrote:
>> Hi,
>>
>> I hope I am not asking a too simple question but I am trying
> replacement has 0 rows, data has 98308
>
> at #09. value[[3L]](cond)
> - value[[3L]]() is local of the calling function
>
> at #08. tryCatchOne(expr, names, parentenv, handlers[[1L]])
> - tryCatchOne() is local of the calling function
>
> at #
Hi.
On Thu, Jun 14, 2012 at 11:42 PM, Tommaso Mazza wrote:
> Hi All,
> this is a trivial question for sure, but please give me an hint.
>
> I have data from the chip in object and from a Genome-Wide Human SNP Array
> 6.0 - Affymetrix and a GeneChip Human Mapping 250K array.
> I would like to get
Mbytes). Also, the above script is run part of the regular system
tests and there we don't run out of memory, but I'll check the memory
usage on my Windows 7 machine when I have time. Regardless, I don't
think it is possible troubleshoot this further.
The good thing though, you can just r
On Thu, Jun 14, 2012 at 10:49 AM, MH wrote:
> Hi All,
> I have my test run almost completed and at the step
> dsCNList <- process(cmtN, verbose=verbose);
> I get the following memory error
> Error: cannot allocate vector of size 95.4 Mb
>
> I am on Windows7, 32bit and have many Gs of storage.
>
>
Hi.
On Tue, Jun 12, 2012 at 1:17 AM, dave wrote:
> Hi,
>
> I hope I am not asking a too simple question but I am trying to load
> affy HuGene-1_1-st-v1 chips on aroma.affymetrix. I have been away from
> affy analysis for a while so maybe this is a known thing. I cannot
> find the corresponding cd
Hi.
Yes, to extract all cell (=probe) intensities from all arrays in an
AffymetrixCelSet ('csN'), you can do:
Y <- extractMatrix(csN, drop=FALSE)
Typically an Affymetrix array contains several million probes, so this
will be a rather big matrix, especially if you have many arrays.
More comments
Hi.
On Wed, Jun 6, 2012 at 9:23 AM, Hyuna Yang wrote:
>
> Hi all,
>
> I have custom array (similar to human Exon array) and try to study
> alternative splicing using FIRMA.
> i) in theory, I think I can use FIRMA, but wonder that's possible at current
> aroma.affymetrix setup.
Yes, given that yo
ed after CBS?
>>
>> Also, my other question is that does PSCBS only give result of all
>> chromosomes together or can we obtain each chromosome result separately?
>> Also, I want to obtain DH, TCN, BAF values, can we write them on a xls file
>> after PSCBS?
>>
>
Hi.
On Sat, May 5, 2012 at 1:12 PM, Sathish Periyasamy
wrote:
> I have completed the doCRMAv2 for tumour/ Normal pairs and obtained
> the results in ChromosomeExplorer. However, I would like to find the
> common variance (i.e. gains and loss, LOH) across these pairs.
>
> I would be pleased if yo
Hi.
On Mon, Apr 30, 2012 at 5:31 AM, Marcin wrote:
> Dear Henrik,
>
> I have a dataset in which my collaborators took two types of cancer
> cell lines and made a few single copy clones of them per cell line.
> The clones were then used for drug resistance study in pairs (i.e.
> clone treated vs c
Hi.
On Wed, May 9, 2012 at 11:40 AM, Yu Song wrote:
> Dear Henrik,
>
> I have one question about CBS output.
I'm not 100% sure what you mean by "CBS output", but I guess that you
are referring to the "regions.xls" files generated by CbsModel - is
that so? There is also the option to get the DNA
Hi,
On Tue, May 8, 2012 at 3:02 PM, Michelle wrote:
>
> Hi Pierre,
>
> Thanks!
> I find that if I use R commands to save the plot, such as this,
>
> toPNG(pairName, tags=c(chrTag, "PairedPSCBS"), width=840, aspectRatio=0.6,
> {
> plotTracks(fit);
> });
>
> The saved plot has poor quality, with
Hi,
there is no direct way to segment only non-polymorphic loci ("CN
probes")/exclude SNPs, but one approach would be to create a custom
UGP annotation data file where the genomic positions for all SNPs as
set to missing (=NA), and then explicitly use that UGP file when
segmenting the data.
/Henr
Hi.
On Fri, May 18, 2012 at 11:17 AM, sean nj wrote:
> Hi, it's me again :)
>
> I have some level 2 TCGA agilent CGH 244A data, the text files of log2
> ratios. I followed vignettes (http://aroma-project.org/node/43 and
> http://www.aroma-project.org/node/88) and created UGP files and data files
Hi.
On Tue, May 8, 2012 at 4:16 AM, Jay wrote:
> Dear Henrik
>
> I am a consultant working with Laurent Malvert.
> Many thanks for helping us with the aroma.affymetrix issue we have
> been experiencing. Gladly this looks like being complete.
> Whilst installing your recent release of aroma.affym
Hi.
On Tue, May 22, 2012 at 3:41 AM, Cristian Bassi
wrote:
> Hi everyone,
> I successfully applied CRMAv2 for estimating copy numbers from a set of 14
> paired samples, and after the segmentation process I used chromosome
> explorer for displaying the results.
> The problem is that the regions po
Hi,
everything is fine; you've got the correct annotation data files. The
only issue is that code writing that 'url' column added to the
regions.xls file is rather stupid, i.e. the genome version is hard
coded.
You can rewrite the regions.xls file with the correct UCSC Genome
Browser by passing
Hi,
some minor corrections/clarifications below.
On Mon, Apr 16, 2012 at 1:32 AM, Pierre Neuvial
wrote:
> 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 (deta
t; [4] LC_NUMERIC=C LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.4.0 affxparser_1.26.4 aroma.apd_0.2.0
> R.huge_0.3.0
> [5]
...and by the way, what is your sessionInfo(), i.e. what does the
following report?
> library("aroma.affymetrix");
> sessionInfo();
/Henrik
On Thu, Apr 5, 2012 at 1:55 PM, Henrik Bengtsson
wrote:
> Hi,
>
> first of all, there is a very simple reason for this, we ju
Hi,
first of all, there is a very simple reason for this, we just have to
find out why. My best guess now is that one of the files are
incomplete. Start a fresh R session and verify that you get the
exactly same *file sizes* as below:
> library("aroma.affymetrix");
> cdf <- AffymetrixCdfFile$by
Hi.
On Wed, Apr 4, 2012 at 7:57 AM, Fred Foucault
wrote:
> Hello,
>
> I want to get allele specific copy number from SNP6 CL files
> I´m following the vignette for ACNE.
> I installed the annotation data in \test\annotationData\chipTypes
> \GenomeWideSNP6.0
The name of that subdirectory is not
Hi,
sorry for the delay on this one. It is seems that you have a special
case that we didn't consider when we designed the naive genotyping
algorithm. I can have a look at this, but in order to do that I'd
need some example data. Would you mind making the data for one
tumor-normal pair available
Hi,
sorry for the delay.
To me it looks like you cannot install any of the packages that are on
CRAN (= 'DEFAULT' in the output). First, try to install 'digest' as
follows:
install.packages("digest")
Verify that it works by loading it, i.e. library("digest"). If it
still doesn't work, please
Hi.
On Mon, Mar 19, 2012 at 12:02 PM, Fong wrote:
> Hi,
>
> I am using SNP6 arrays right now and I've got an annotationData directory
> that looks like this:
>
> GenomeWideSNP_6,Full.cdf
> GenomeWideSNP_6,Full,monocell.CDF
> GenomeWideSNP_6,HB20080710.acs
> GenomeWideSNP_6,Full,na24,hg18,HB200802
Hi,
aroma.affymetrix v2.5.0 and friends have been updated. Update by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
The main update in this release is on the ArrayExplorer v3.4 and
ChromosomeExplorer v3.4, which can now be viewed (both locally and
onlin
10333
> 1721179 1723017 1729405 1730585 1730735 1731525 1739661 1746525
> 1747313 1755855 1763977 1764777 1765030 1765442 1768608 1785894
> 1789920 1795485 1800601 1808317 1817968 1824273 1825969 1826711
> 1833963 1834098 1834857 1835588 1837249 1840230 1841309 1841721
> 1842323 1842491
On Fri, Mar 9, 2012 at 11:40 AM, Gregory W wrote:
> From trial and error I see I can simply use the function:
>
> AromaUnitTotalCnBinarySet()
>
> and pass it my list of files.
Yes, i.e.
files <- list(...);
ds <- AromaUnitTotalCnBinarySet(files);
(I think) you can also create an empty data set a
Hi Laurent.
On Thu, Mar 8, 2012 at 6:13 AM, Laurent Malvert wrote:
> On Thursday, February 2, 2012 4:47:34 AM UTC, Henrik Bengtsson wrote:
>> [...]
>
>> When time permits, I'll also update ArrayExplorer (which still only
>> works in Firefox 3.x).
>
> Hello Hen
ition: Warning messages:
> 1: In FUN(X[[1L]], ...) : NaNs produced
> 2: In FUN(X[[1L]], ...) : NaNs produced
> -------
> So that there is only dfn[1] created, not dfn[2]...dfn[20].
>
ame. Do you think it might be the problem with too many
> patients(20)?
>
> Thanks a lot for your help!
> Yu
>
> On Mon, Mar 5, 2012 at 2:29 PM, Henrik Bengtsson
> wrote:
>> Hi Yu,
>>
>> the quick answer is that your file has been successfully written, but
>
Hi.
On Fri, Mar 2, 2012 at 1:37 AM, hiberbear wrote:
> Hi everyone:
>
> I am running aroma.affymetrix on human exon array (HuEx-1_0-st-v2). I find a
> confusing thing about the gene summary:
> trFit is identical to ExFit.
> My understanding is that if mergeGroups=TRUE, I may get a single value f
taFrame() [at the very
end] to assert that the generated file can be properly parsed by R.
Because you have '#' in your filenames, which becomes column names,
the assertion test identifies a "conflict" with column names having
'#":s and the file header comments starting with '#':s. I've
overlooked this use case, and I'll add it to the todo list to either
detect & warn
Hi.
On Fri, Mar 2, 2012 at 8:52 AM, Yu Song wrote:
> Dear Mr.Bengtsson,
>
> I am trying to create a data containing the "unitName", "chromosome"
> and "position" from the output CEL of preprocessing.
What type of CEL files? What type of preprocessing?
/H
> Is there a certain command to do thi
Hi.
On Tue, Feb 28, 2012 at 3:46 AM, Saif UrRehman wrote:
> Hi guys,
>
> I am trying to normalise 5000 HG-U133A celfiles using the aroma library it
> seems to run fine.
>
> However it stopped reading in Celfiles after 2,246 files after about 11
> hours. It appears to fail silently.
Ouch, I hope
Hi,
On Fri, Feb 17, 2012 at 1:44 PM, Michelle wrote:
> Hi Henrik,
>
> I ran the PSCBS package on some Affy SNP 6.0 arrays. In the output I found
> that several files contain a few lines of negative "tcnMean" values, while
> the rest are all positive. My question is - the total copy number is
> su
h = path, ...)
> at getReadablePathname(static, path = path, ...)
> at method(static, ...)
> at Arguments$getReadablePath("rawData/C11/GenomeWideSNP_6/")
>
>
> Many thanks,
> Angelina
>
> From: aroma-affymetrix@google
On Sun, Feb 12, 2012 at 5:18 PM, sigrid wrote:
> Hello,
>
> I would like to know if my tumor sample is mutated compared to my
> normal sample for a specific gene.
Do you mean mutations of individual nucleotides?
/Henrik
>
> Thank you!.
>
> Sigrid
>
> On 1
Hi,
I suspect you're asking for something that is not possible, so can you
clarify/define what you mean by "mutations"?
/Henrik
On Sun, Feb 12, 2012 at 5:06 PM, sigrid wrote:
> Hi,
>
> I have successfully run TumorBoost on my samples. I would like to
> retrieve the mutations from this (for a pa
Hi,
originally those data files were only available on a DVD that you had
to order from Affymetrix, whereas now you'll find *similar* data files
from the the HapMap Project itself. AFAIK, we are not allowed to
redistribute. Even if you cannot find the exact same samples at
HapMap, you can use any
Hi Jean-Paul.
On Fri, Feb 10, 2012 at 3:05 AM, Jean-Paul Abbuehl wrote:
> Hi
>
> I am a total newbie with R analysis and this is my first analysis I am
> doing with Aroma.
> I am getting the same error repetitively after following instruction on the
> project website.
> I have the last R version
Hi Irsan,
so a quick background: (i) it is important that document is in sync
with the software and not outdated, (ii) it is very time consuming to
make sure is the case, and (iii) even more so to provide rich/detailed
documentation. Since there are very limited resources, the strategy
in aroma i
; but could you please advise what I should do?
>
> Kind regards,
> Angelina
>
>
>
> From: aroma-affymetrix@googlegroups.com [aroma-affymetrix@googlegroups.com]
> On Behalf Of Henrik Bengtsson [henrik.bengts...@aroma-project.o
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