Before anything else, can you verify that your CDF is correct?
Confirm that you get the following:
> library("aroma.affymetrix");
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6
Just a mistake. Thanks for spotting it. /Henrik
On Mon, Jul 23, 2012 at 4:36 PM, complexkid wrote:
> Hi Henrik,
> I just noticed your response in the thread :
> https://groups.google.com/forum/#!msg/aroma-affymetrix/RCHLDIfO47s/SJafAcaQnZsJ.
> Why is the following operation done twice ?
>
>
> htt
On Wed, Aug 1, 2012 at 11:31 AM, Fong wrote:
> Hi,
>
> I seem to be unable to figure out whether this question has been addressed
> or not so I apologize if this has already been asked. Basically I have a
> set of U133 arrays which I have processed through aroma.affymetrix and now I
> am just usi
Hi,
I'm not sure what is going on. It should certainly not get stuck for
14 hours, unless you're running out of RAM and you're swapping like
crazy, but that should not happen if you have, say, at least 1GB of
RAM. Are you doing this in a fresh R session?
Where it seems to hang has nothing to do
Hi,
I see nothing wrong with your script. I suspect that the CDF you've
downloaded got corrupted or something. Do you get the same output as
below:
> library("aroma.affymetrix")
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags = "coreR3,A20071112,EP");
> cdf
## AffymetrixCdfFile:
## Path: a
Hi,
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,
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
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
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
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
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
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.
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
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
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()
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.
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
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,
> 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
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
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
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
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.
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
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,
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
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
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,
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
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,
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,
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,
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
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,
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
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
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
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
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
>
>
>
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)
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.
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
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
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
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
eed 1.1GB and with
RAM=1.0 it will use up to 1.7GB of RAM.
How much RAM/memory do you have on your computer?
/Henrik
>
>
>
>
>
>
> At 2012-11-27 13:57:24,"Henrik Bengtsson-4 [via aroma.affymetrix]" <[hidden
> email]> wrote:
>
> Hi,
>
> first thing
70 216.7 83594476 637.8 130588565 996.4
> Fitting 1 arrays...done
> Estimating single-probe CN units...done
>> str(units1);
> int [1:945826] 935590 935591 935592 935593 935594 935595 935596 935597
> 935598 935599 ...
>> units <- findUnitsTodo(plm);
>> str(units);
ever, there was a bug in the version you
used causing only setRam() to work, which is why I told you to use
that one. If you install the latest version:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
you should also get aroma.core v
1.50
> Number of QC units: 4
>> stopifnot(identical(getChecksum(cdfM),
>> "3a797e24a62f4f2e5214a6bf819151da"));
>> getChecksum(cdfM)
> [1] "3a797e24a62f4f2e5214a6bf819151da"
>
> Ioana
>
> On Tuesday, 27 November 2012 21:40:54 UTC+2, Henrik Bengtsson wrote:
>>
[I'm reply to each of your questions in three separate threads to make
it easier to follow]
Hi.
On Fri, Nov 30, 2012 at 12:44 PM, Sam Danziger wrote:
> I've been trying to use FIRMA analysis
> (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my
> mouse arrays (
> Mouse Ex
On Fri, Nov 30, 2012 at 12:44 PM, Sam Danziger wrote:
> I've been trying to use FIRMA analysis
> (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my
> mouse arrays (
> Mouse Exon 1.0 ST Array -
> http://aroma-project.org/chipTypes/MoEx-1_0-st-v1).
>
> It looks like the scri
Hi again.
On Fri, Nov 30, 2012 at 12:44 PM, Sam Danziger wrote:
> I've been trying to use FIRMA analysis
> (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my
> mouse arrays (
> Mouse Exon 1.0 ST Array -
> http://aroma-project.org/chipTypes/MoEx-1_0-st-v1).
>
> It looks li
On Thu, Dec 6, 2012 at 5:54 AM, Maria Traka wrote:
> Hi guys,
> probably you've already given the answer somewhere but can i use
> aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)?
> Presumably the same way as 1.0 arrays?
I'm not working with those myself, and I don't know t
such. (*) BTW, that script has
now been replaced by
http://aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo
Thanks,
Henrik
> HTH,
> Guido
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymetrix@googlegroups.com] O
On Fri, Dec 7, 2012 at 2:09 PM, Hooiveld, Guido wrote:
> Hi,
> Sorry for the indistinctness. You are correct; these are indeed R-packages
> (CDF environments), thus not *files*. However, it won't be much effort to
> also make them available as files. I/we will have a look at it the next
> coupl
Hi.
On Fri, Dec 7, 2012 at 7:04 PM, zhouzaiwei wrote:
> Hi, everyone, I want to use FIRMAGene to analysis differencial splicing of
> hugene-1.0-st array ,there is no overlap between Ensembl identifiers from
> getUnitNames() and Affymetrix identifiers in 'hgnetaffx'.follows my code:
>>library(arom
Hi.
On Mon, Dec 10, 2012 at 8:49 AM, Hooiveld, Guido wrote:
> Hi Henrik,
>
>
>
> I am testing the binary CDF files I created for various Gene ST arrays (re:
> discussion last Friday), but I run into problems.
>
> An error is occurring when reading the cell files. According to the change
> log thi
Hi all,
aroma.affymetrix v2.8.0 has been released. Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Bug fixes, improved fault tolerance, more unique caching, improved
creation of CDF files from Bioconductor PDInfo packages and more. As
usual, details b
Hi.
On Thu, Jan 3, 2013 at 12:11 AM, Saman Amini wrote:
>
> Hi all,
>
> I am using aroma.affymetrix to get the segmented paired copy numbers for raw
> CELL files and CDF annotation files. The path and the R script are shown
> below.
> As you can see in the result table, the last column is showi
What's your session info after loading aroma.affymetrix and calmate?
Henrik
On Jan 4, 2013 9:59 PM, "Zheng Siyuan" wrote:
>
> Hi,
> I have been using Calmate to process my affy SNP6 array data. The goal is
to call calibrated allele specific copy number. However, I ran into an
error following the
R.filesets_1.9.0
> [16] R.utils_1.19.3 R.oo_1.11.4R.methodsS3_1.4.2
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.0 PSCBS_0.30.0
>
> Have you seen this before?
> Thanks.
>
> Siyuan
> MD Anderson
>
>
>
> On Friday, Janu
Try with calmate v0.10.0, which you can install by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("calmate")
Let me know if this solves it for you.
/Henrik
On Fri, Jan 4, 2013 at 3:32 PM, Siyuan Zheng wrote:
> Thank you.
>
>
> On Fri, Jan 4, 2
Just to close this (old) thread:
On Mon, May 7, 2012 at 1:07 PM, sean nj wrote:
> Hi guys,
>
> I tried to convert recent customCDF HTHGU133A_Hs_ENTREZG.cdf (version 15.10)
> to binary format and end up with error message:
>
> Error in convertCdf("HTHGU133A_Hs_ENTREZG.cdf",
> "HTHGU133A_Hs_ENTREZG
On Mon, Feb 4, 2013 at 4:14 PM, wrote:
> Hi All,
>
> I was following the online viginette
> http://www.aroma-project.org/howtos/exportTotalCnRatioSet to export total
> Copy Number Ratios, i have ran CRMAv2 without problem, but when I try to do
> the following i got the error in cdf, anyone ha
Hi,
sorry for the delay - I've been "off the grid" since two weeks.
On Thu, Jan 24, 2013 at 4:09 AM, Oscar Rueda wrote:
> Dear all,
>
> I'm trying to run PSCBS on 126 matched pairs, but only 60 of them have run
> without errors. The last error I got was when running callAB:
>
>> deltaAB <- estim
On Thu, Feb 7, 2013 at 5:33 PM, Henrik Bengtsson
wrote:
> Hi,
>
> sorry for the delay - I've been "off the grid" since two weeks.
>
> On Thu, Jan 24, 2013 at 4:09 AM, Oscar Rueda
> wrote:
>> Dear all,
>>
>> I'm trying to run PSCBS on 12
Hi "CK",
On Fri, Feb 1, 2013 at 6:56 AM, wrote:
> Hi,
>
>i am a new user of aroma.affymetrix , can I know how do one export
> intensity values from all the samples into matrix form? ( i have 57 CEL
> files), since i would like to use those to perform pca and check for batch
> effect.
If you
ellow, Caldas Lab, Breast Cancer Functional
> Genomics.
> University of Cambridge. Cancer Research UK Cambridge Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
> England
>
> Please note that my email address will be changing to:
> oscar.ru...@cruk.cam.ac.uk
unctional
> Genomics.
> University of Cambridge. Cancer Research UK Cambridge Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
> England
>
> Please note that my email address will be changing to:
> oscar.ru...@cruk.cam.ac.uk
>
>
>
>>
>&
Hi Ingrid.
On Wed, Mar 20, 2013 at 4:45 PM, Ingrid Lönnstedt
wrote:
>
> Hi!
>
> I have segmented 56 SNP 6 tumour samples with segmentByNonPairedPSCBS(),
> and like to call allelic balance segments with callAB() as required, I
> understand, before I can call neutral TCNs with callNTCN().
First, I
Hi Carles,
the quick answer it that aroma.affymetrix only implements the CRLMM
method for the 100K (Mapping50K_Xba142 and Mapping50K_Hind142) and
500K (Mapping250K_Nsp and Mapping250K_Sty) chip types. For newer
methods you need to turn to the Bioconductor 'oligo' package.
However, what are you
I can reproduce this - very odd. I'll investigate a fix it. In the
meanwhile, install the aroma.* 2.8.0 versions via CRAN, e.g.
install.packages("aroma.core", repos="@CRAN@")
install.packages("aroma.affymetrix", repos="@CRAN@")
(Add repos="@CRAN@" to make sure not to install from other repositor
Install() to never install from R-forge. FYI, don't install
from R-forge, because that contains my non-official under-construction
and non-tested updates.
On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson
wrote:
> I can reproduce this - very odd. I'll investigate a fix it. In the
>
ma.affymetrix], or (b) GenomeWideSNP_(5|6) [which is not ported].
In other words, it's the internal oligo:::genotypeOne() that needs to
be ported.
>
> Anyway, thank you to share with us the aroma.affymetrix suite.
You're welcome - hopefully it makes everyday science a bit easier.
/Henrik
&g
57941, GSM557942
> Color maps: sqrt,yellow
> Chip type: GenomeWideSNP_6.Full
> Samples: GSM557940, GSM557941, GSM557942
> Aliases: GSM557940, GSM557941, GSM557942
> [1] FALSE
>
>
> Uma
>
> On Sat, Mar 23, 2013 at 5:05 PM, Henrik Bengtsson
> wrote:
>>
>&g
<- Arguments$getVerbose(-8, timestamp=TRUE)
I've changed 'log' to 'verbose', because that will always work.
/H
>
> Thx
>
> Uma
>
>
> On Sat, Mar 23, 2013 at 5:32 PM, Henrik Bengtsson
> wrote:
>>
>> On Sat, Mar 23, 2013 at 2:29 PM, Uma Sha
M: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
>
> Thanks in advance
> Uma
>
> On Sat, Mar 23, 2013 at 5:52 PM, Uma Shankavaram
> wrote:
>>
>> Sorry, I guess I overlooked it. Many thanks for the help.
>>
>> Uma
>>
>>
>> On Sat, Mar 23, 201
ld me, but are you working
with fresh frozen tumors or FFPE ones? The latter are often messy and
I haven't seen any methods that rescue their signals very well.
/Henrik
> All the best,
> Ingrid
>
>
> On Saturday, 23 March 2013 05:03:50 UTC+11, Henrik Bengtsson wrote:
>>
Hi Jonathan.
On Thu, Apr 11, 2013 at 6:38 AM, wrote:
> Hi all,
>
> I suppose this is a simple enough task even for a newbie like me, I have
> found a similar related post but I have two questions:
>
> My First Question when I use the following commands in R:
>
> library(aroma.affymetrix)
>
> cdf
this. See a couple of remaining issues below.
> /Ingrid
>
>
>
> On Wednesday, 27 March 2013 18:16:07 UTC+11, Henrik Bengtsson wrote:
>>
>> On Tue, Mar 26, 2013 at 10:03 PM, Ingrid Lönnstedt
>> wrote:
>> >
>> > Thank you Henrik!
>> &
d on bootstrapped segment TCN levels
fit <- callNTCN(fit, delta=deltaCN, verbose=-20);
printf("Number of NTCN segments: %d\n", sum(getSegments(fit)$ntcnCall,
na.rm=TRUE));
## Number of NTCN segments: 303
toPNG(sampleName, tags="tracks,avgDH=median,AB+LOH+NTCN", aspectRatio=
gt; Today's Topic Summary
>>Group:
>>http://groups.google.com/group/aroma-affymetrix/topics
>><http://groups.google.com/group/aroma-affymetrix/topics>
>>
>>* PSCBS and callNTCN() (Was: Re: [aroma.affymetrix] Digest for
>>aroma-affymetrix@googleg
Hi,
sorry for the long delay.
On Mon, Apr 1, 2013 at 7:21 AM, wrote:
> Dear forum,
>
> I am analyzing data of HuGene2.0-st arrays. I am using aroma for
> pre-processing and used limma for differential expression. However after
> multiple testing I lost significance so I want to perform variance
a$cell);
# Merge CDF annotation data with signals
data <- cbind(cdfData, Y);
# Save
# [see help("writeDataFrame.data.frame")]
pathname <- writeDataFrame(data, file="all_probes.txt",
header=list(chipType=getChipType(cdf)));
Again, not sure what you're go
Hi.
On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED wrote:
> hi Pierre,
>
> the anootationData is allocated by default in the aroma.affymetrix ?? is it
> ??? as its declare in the page of aroma :
>
> Aroma.affymetrix searches for CDF files in the annotationData/ directory of
> the current w
rguments$getReadablePath("AromaAnalysis/annotationData/HG-U133_Plus_2",
> mustExist = TRUE)
> - Arguments$getReadablePath() is local of the calling function
>
> Error: Pathname not found: AromaAnalysis/annotationData/HG-U133_Plus_2 (none
> of the parent dir
Hi all,
aroma.affymetrix v2.9.0 has been released and is available on CRAN
(where the package is hosted). Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This is mainly a maintenance update to meet some new CRAN
requirements. Interestingly, no bugs w
Hi Yadav,
thanks for reporting on this. It to me a while to reproduce it. A
quick fix would be to explicitly load the R.cache package, which is
the package that defines that missing getChecksum(). However, I've
fixed this in aroma.core v2.9.2, so you update the error should go
away. Update as
Hi.
On Wed, May 29, 2013 at 3:12 AM, shangzhong Li wrote:
> I am trying to analyse GSE 30321 datasets in R. However it has 295 samples
> in two files (one has 255 and another has 40). They have same platform.
> gset <- getGEO('GSE30321',GSEMatrix =TRUE)
> gives gset two elements. Does anyone kno
Hi,
I've done some updates to the help pages (e.g. ?doCBS), so before
anything I recommend to update to aroma.core 2.9.5 and
aroma.affymetrix 2.9.4:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
On Tue, May 28, 2013 at 9:37 AM, Wei Tang wrote:
> Hi aroma.affymetr
ysis analysis
> because QuantileNormalization could affect the relationship between pairs of
> coexpressed genes.
>
> If not, could you suggest me another package I could use? Is limma my only
> option ?
> Looking forward hearing from you
> Best
>
> Jean-paul.
>
> Le jeudi 13 août
f you plan to infer parent-specific CNs. If you don't know
yet, use doASCRMAv2(). Everything should work the same with doCBS().
/Henrik
>
> Many thanks,
>
> Wei
>
>
> On Thursday, May 30, 2013 6:05:55 PM UTC-4, Henrik Bengtsson wrote:
>>
>> Hi,
>>
&g
raphics grDevices utils datasets methods base
>
> other attached packages:
> [1] R.cache_0.6.5 aroma.cn_1.3.3 DNAcopy_1.34.0
> [4] aroma.affymetrix_2.9.4 affxparser_1.32.1 aroma.apd_0.2.3
> [7] R.huge_0.4.1 aroma.light_1.30.2 aroma.core_2
tal" "E1520T_Nsp,total"
>> [4] "E1521T_Nsp,total" "E1532T_Nsp,total" "E1535T_Nsp,total"
>> [7] "E1542T_Nsp,total" "E1546T_Nsp,total" "E1558T_Nsp,total"
>> [10] "E1566T_Nsp,total" &quo
rt that they have the same number of samples:
# [doCBS() will do this too]
stopifnot(length(dsTTuple) == length(dsNTuple));
# Matched tumor-normal segmentation (pay attention to the verbose at
the beginning)
doCBS(dsTTuple, ref=dsNTuple, verbose=-10);
Hope this helps
Henrik
>
> Many thanks,
>
of the Paired PSCBS (PDF)
vignette that is part of the PSCBS package.
/Henrik
>
>
> Many thanks,
>
> Wei
>
>
> On Thu, Jun 6, 2013 at 5:38 PM, Henrik Bengtsson
> wrote:
>>
>> On Thu, Jun 6, 2013 at 1:43 PM, Wei Tang wrote:
>> > Everything goes very
I thought I fixed this in aroma.core 2.9.2, but I guess it wasn't enough.
For now try to load the R.cache package on startup - that should work
around the problem. Let me know if it works.
Henrik
On Jun 20, 2013 5:46 PM, "rangerq" wrote:
> Hi,
>
> I got an error when I processed a Affy Human Ge
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
> attached base p
On Wed, Jun 12, 2013 at 9:56 PM, Wei Tang wrote:
> Hi Henrik,
>
> Would you tell me where I can find the information of human build for the
> arrays?
> it seems you used hg18? am I correct?
Which genome version you use depends on which annotationData/ files
you use. Here are the ones we've built
Hi,
see http://aroma-project.org/howtos/ImproveProcessingTime
Most importantly, increasing the RAM option will make a big difference.
/Henrik
On Mon, Jul 15, 2013 at 11:05 PM, Ryan Chow wrote:
> Hello,
>
> I'm looking to process 4000 HG-U133_Plus_2 microarrays using aroma, as it is
> memory-bo
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