[BioC] [SPAM?] Bioconductor Digest, Vol 41, Issue 22 (Out of Office)
Todd Nick
Todd.Nick at cchmc.org
Sat Jul 22 12:01:29 CEST 2006
I'm out of the office until July 28th. Please contact liz higgins if you
need assistance @ 636-0163.
>>> bioconductor 07/22/06 06:00 >>>
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Today's Topics:
1. MySQL databases offering gene expression, esp. toxicogenomics
data (N. Goodacre)
2. Error: cannot allocate vector of size ... (Wall, Dennis Paul)
3. Re: MySQL databases offering gene expression, esp.
toxicogenomics data (Arne.Muller at sanofi-aventis.com)
4. Re: Error: cannot allocate vector of size ... (James W. MacDonald)
5. Re: Error: cannot allocate vector of size ... (M L Smith)
6. Re: ABPackageBuilder not building GO package? (Nianhua Li)
7. Re: Error: cannot allocate vector of size ... (Levi Waldron)
8. Re: MySQL databases offering gene expression, esp.
toxicogenomics data (Seth Falcon)
9. artifact in MA plots (Matthew Scholz)
10. error in simpleaffy qc: I'm sorry, I do not know about chip
type: poplarcdf (Levi Waldron)
11. Re: Missing chromosomal locations in hgu133a package (John Zhang)
12. Problem regardign ReadAffy() (Nayeem Quayum)
13. Re: Missing chromosomal locations in hgu133a package (Nianhua Li)
14. Re: ABPackageBuilder not building GO package? (Eric J. Kort)
15. Re: ABPackageBuilder not building GO package? (Nianhua Li)
16. Quick illumina question (Sean Davis)
17. Re: Quick illumina question (Oosting, J. (PATH))
----------------------------------------------------------------------
Message: 1
Date: 21 Jul 2006 03:36:08 +0100
From: "N. Goodacre" <ng296 at cam.ac.uk>
Subject: [BioC] MySQL databases offering gene expression, esp.
toxicogenomics data
To: bioconductor at stat.math.ethz.ch
Message-ID: <Prayer.1.0.17.0607210336080.10500 at hermes-2.csi.cam.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1
Dear Bioconductor mailing group,
I would like to ask if anyone knows of a solid toxicogenomics database
under MySQL - i.e. one with expression profiles for a number of
toxicities.
If it helps, the toxicities I am interested in are hepatotoxicities. I
am a
little shaky on just who gets to use MySQL and who does not, especially
for
Bioinformatians, so perhaps if someone could run over this for me, that
would be greatly appreciated as well.
Sincerely,
Norman Goodacre
------------------------------
Message: 2
Date: Fri, 21 Jul 2006 07:55:18 -0400
From: "Wall, Dennis Paul" <dennis_wall at hms.harvard.edu>
Subject: [BioC] Error: cannot allocate vector of size ...
To: "Bioconductor" <bioconductor at stat.math.ethz.ch>
Message-ID:
<3F9010CC205E6F49B4165C01C4B344FDC0AB49 at MAILSERVER01.MED.HARVARD.EDU>
Content-Type: text/plain; charset="us-ascii"
I am trying to run the pam algorithm for k-means clustering, but keep
getting the error "Error: cannot allocate vector of size 1048384 K"
Any help on how to fix this would be greatly appreciated.
Cheers,
Dennis
------------------------------
Message: 3
Date: Fri, 21 Jul 2006 18:04:05 +0200
From: <Arne.Muller at sanofi-aventis.com>
Subject: Re: [BioC] MySQL databases offering gene expression, esp.
toxicogenomics data
To: <ng296 at cam.ac.uk>, <bioconductor at stat.math.ethz.ch>
Message-ID: <C80ECAFA2ACC1B45BE45D133ED660ADE02E8CC5B at CRBSMXSUSR04>
Content-Type: text/plain; charset="iso-8859-1"
Hello,
I don't know about any mysql db for toxicogenomics but I guess you're
interested in the data rather than the underlying database software.
There's the ILSI project on collecting toxicogenomics data together with
classical toxicology measures. Check www.ilsi.org and search for
toxicogenomics (actually it does not return much ...).
We've participated in this cross-institutional/company project and
submitted our data to ArrayExpress at the EBI, others have submitted
theirs to GEO at the NCBI. You could look for 'ILSI' related projects in
there. ArrayExpress returns 14 experiments.
Sounds like a big project to gather all this data in areasonable way ...
I know that GeneLogic offers a commercial database with in-house
generated expression data + toxicities for several reference compounds
in several tissues.
hope this helps,
+regards,
Arne
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of N. Goodacre
Sent: Friday, July 21, 2006 04:36
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] MySQL databases offering gene expression,esp.
toxicogenomics data
Dear Bioconductor mailing group,
I would like to ask if anyone knows of a solid toxicogenomics database
under MySQL - i.e. one with expression profiles for a number of
toxicities.
If it helps, the toxicities I am interested in are hepatotoxicities. I
am a
little shaky on just who gets to use MySQL and who does not, especially
for
Bioinformatians, so perhaps if someone could run over this for me, that
would be greatly appreciated as well.
Sincerely,
Norman Goodacre
_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
------------------------------
Message: 4
Date: Fri, 21 Jul 2006 11:48:06 -0400
From: "James W. MacDonald" <jmacdon at med.umich.edu>
Subject: Re: [BioC] Error: cannot allocate vector of size ...
To: Bioconductor <bioconductor at stat.math.ethz.ch>
Message-ID: <44C0F736.1030702 at med.umich.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed
Wall, Dennis Paul wrote:
> I am trying to run the pam algorithm for k-means clustering, but keep
> getting the error "Error: cannot allocate vector of size 1048384 K"
>
> Any help on how to fix this would be greatly appreciated.
That error means you are running out of RAM. The quickest, best fix is
to get more.
Best,
Jim
>
>
> Cheers,
>
> Dennis
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues.
------------------------------
Message: 5
Date: Fri, 21 Jul 2006 17:24:16 +0100
From: "M L Smith" <mls40 at cam.ac.uk>
Subject: Re: [BioC] Error: cannot allocate vector of size ...
To: Bioconductor at stat.math.ethz.ch
Message-ID: <44C10DC0.14668.1308575 at localhost>
Content-Type: text/plain; charset=US-ASCII
Hi Paul,
If you've followed that advice or you've already got plenty of RAM
you can try the command:
memory.limit(2048)
This should allow R to use 2Gb of RAM (the max it can use on a
normal Windows machine), rather than the 1Gb it defaults too.
Mike Smith
> Wall, Dennis Paul wrote:
> > I am trying to run the pam algorithm for k-means clustering, but
keep
> > getting the error "Error: cannot allocate vector of size 1048384K"
> >
> > Any help on how to fix this would be greatly appreciated.
>
> That error means you are running out of RAM. The quickest, best
fix is
> to get more.
>
> Best,
>
> Jim
>
>
> >
> >
> > Cheers,
> >
> > Dennis
> >
> > _______________________________________________
--
Computational Biology Group
Hutchison / MRC Research Centre
Department of Oncology
University of Cambridge
Hills Rd, Cambridge CB2 2XZ
Email: mls40 at cam.ac.uk
------------------------------
Message: 6
Date: Fri, 21 Jul 2006 16:09:53 +0000 (UTC)
From: Nianhua Li <nli at fhcrc.org>
Subject: Re: [BioC] ABPackageBuilder not building GO package?
To: bioconductor at stat.math.ethz.ch
Message-ID: <loom.20060721T175858-725 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii
Hi, Eric,
The "error" messages about KEGG urls are not really errors, so you can
ignore
them. And the information about removing datasets are normal messages as
well.
Could you please try:
ABPkgBuilder(baseName="keyp.txt", baseMapType="gb", pkgName="vaimm06",
pkgPath="./", organism="Mus musculus", version="0.1",
author=list(author="Eric
J. Kort", maintainer="Eric J. Kort"))
It is the same as your code except that "srcUrls" is removed. Let me
know if it
doesn't work
thanks
Nianhua Li
Computational Biology, PHS, FHCRC
------------------------------
Message: 7
Date: Fri, 21 Jul 2006 12:43:51 -0400
From: "Levi Waldron" <levi.waldron at utoronto.ca>
Subject: Re: [BioC] Error: cannot allocate vector of size ...
To: Bioconductor at stat.math.ethz.ch
Message-ID:
<7a09e3940607210943n25136f7bkc2f947835383cecc at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8; format=flowed
I'm not sure if this will help, but this is an exerpt from the affy
vignette:
5. Read in the data and create an expression, using RMA for example.
R> Data <- ReadAffy() ##read data in working directory
R> eset <- rma(Data)
Depending on the size of your dataset and on the memory available to
your system, you might experience errors like 'Cannot allocate vector
. . . '. An obvious option is to increase the memory available to your
R process (by adding memory and/or closing external applications2 . An
another option is to use the function justRMA.
R> eset <- justRMA()
This reads the data and performs the 'RMA' way to preprocess them at
the C level.
One does not need to call ReadAffy, probe level data is never stored
in an A?yBatch. rma continues to be the recommended function for
computing RMA.
------------------------------
Message: 8
Date: Fri, 21 Jul 2006 10:29:41 -0700
From: Seth Falcon <sfalcon at fhcrc.org>
Subject: Re: [BioC] MySQL databases offering gene expression, esp.
toxicogenomics data
To: bioconductor at stat.math.ethz.ch
Message-ID: <m2bqri7toa.fsf at ziti.local>
Content-Type: text/plain; charset=us-ascii
"N. Goodacre" <ng296 at cam.ac.uk> writes:
> Dear Bioconductor mailing group,
>
> I would like to ask if anyone knows of a solid toxicogenomics
database
> under MySQL - i.e. one with expression profiles for a number of
> toxicities.
I'm not aware of such a database.
> I am a little shaky on just who gets to use MySQL and who does not,
> especially for Bioinformatians, so perhaps if someone could run over
> this for me, that would be greatly appreciated as well.
I'm not sure what you mean. Anyone who knows how gets to use MySQL.
MySQL is released under the GPL. Is that your question?
+ seth
------------------------------
Message: 9
Date: Fri, 21 Jul 2006 11:20:54 -0700
From: "Matthew Scholz" <schmatthew at gmail.com>
Subject: [BioC] artifact in MA plots
To: bioconductor at stat.math.ethz.ch
Message-ID:
<3035b8df0607211120n6b2dd0bo571d4b67e14a60d7 at mail.gmail.com>
Content-Type: text/plain
Hi all,
I have some data (10 arrays with ~25000 features each, hybed in a loop
design) that I wanted to background correct because of apparent
non-linearities observed in MA plots. After applying a kooperberg
correction, I replotted the data and noticed that while the overall set
was
much "tighter" and more linear than before correction, a new artifact
appeared in the plots. Namely, rather than all plotting on a horizontal
line, the data took the shape of the open jaw of a shark, with the upper
jaw
horizontal as it should be but a lower jaw of data sloping downward from
the
horizonal at a 45 degree angle. This was all lower intensity data that
plotted in the under 10 log-units region of the MA plot. I tried simple
background subtraction, but this did not eliminate the non-linearities I
originally observed.
I dont' really understand this message as these were nice hybs with
backgrounds around 100-150 RFU, average signals around 4000RFU and no
notable irregularities. Can anyone advise me?
Thanks in advance of your reply,
Matt
--
Matt Scholz
Senior Research Specialist
Department of Plant Sciences
University of Arizona
(520) 621-1695
[[alternative HTML version deleted]]
------------------------------
Message: 10
Date: Fri, 21 Jul 2006 16:13:27 -0400
From: "Levi Waldron" <levi.waldron at utoronto.ca>
Subject: [BioC] error in simpleaffy qc: I'm sorry, I do not know
about
chip type: poplarcdf
To: bioconductor at stat.math.ethz.ch
Message-ID:
<7a09e3940607211313u1332cdcdycc537e4705c364d8 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> library(simpleaffy)
> x <- read.affy("covdesc")
> x.mas5 <- call.exprs(x,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
......done.
scaling to a TGT of 100 ...
Scale factor for: bot0343.CEL 1.19431517356046
Scale factor for: bot0344.CEL 1.25599200206275
Scale factor for: bot0345.CEL 1.72226407855678
Scale factor for: bot0340.CEL 1.45162850888082
Scale factor for: bot0341.CEL 0.960621730495837
Scale factor for: bot0342.CEL 1.34367816094756
> qc <- qc(x,x.mas5)
Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
chip type: poplarcdf
Note that in the sessionInfo() output below I have simpleaffy 2.4.2
which was installed by biocLite. Afterwards I manually upgraded
simpleaffy to 2.6.0, which had no effect.
Any suggestions?
> cdfName(raw.data)
[1] "Poplar"
> sessionInfo()
Version 2.3.1 (2006-06-01)
i486-pc-linux-gnu
attached base packages:
[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices"
[7] "utils" "datasets" "base"
other attached packages:
poplarcdf simpleaffy genefilter survival affy affyio
Biobase
"1.12.0" "2.4.2" "1.10.1" "2.26" "1.10.0" "1.0.0"
"1.10.1"
after upgrading simpleaffy:
> sessionInfo()
Version 2.3.1 (2006-06-01)
i486-pc-linux-gnu
attached base packages:
[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices"
[7] "utils" "datasets" "base"
other attached packages:
poplarcdf simpleaffy genefilter survival affy affyio
Biobase
"1.12.0" "2.6.0" "1.10.1" "2.26" "1.10.0" "1.0.0"
"1.10.1"
------------------------------
Message: 11
Date: Fri, 21 Jul 2006 16:38:26 -0400 (EDT)
From: John Zhang <jzhang at jimmy.harvard.edu>
Subject: Re: [BioC] Missing chromosomal locations in hgu133a package
To: jzhang at jimmy.harvard.edu, hilmar.berger at imise.uni-leipzig.de,
bioconductor at stat.math.ethz.ch
Message-ID: <20060721203826.2E5D64CCD9 at pascal.dfci.harvard.edu>
Content-Type: TEXT/plain; charset=ISO-8859-1
>>>thanks for Your answer. I'm aware of the fact I could create
annotation
>>>packages on my own using AnnBuilder. However, the comparison I
mentioned
>>>was of GoldenPath data and annotation packages of about the same date
>>>(mid 2005), and even current annotation packages show this
discrepancy
>>>in the number of chromosomal locations provided in hgu133a. So I
>>>wondered if there is some good reason to not provide chromosomal
>>>locations for some probesets (e.g. unreliable mappings in GoldenPath)
or
>>>if this is because of special paths AnnBuilder uses to merge all
sources.
>>
There may be two reasons.
1. AnnBuilder uses RefLink.txt and RefGene.txt from Golden Path for
annotation.
Location data were missing from the file for some of the
genes/probes(ie.
8847/216856_s_at) in a test run. Need to talk to Golden Path about htis.
2. The base file used to build the annotation package may not be in sync
with
the current probe-GB mapping provided by AffyMetrix. Nianhua, do you
know if a
fresh download from AffyMetrix was used for release 1.8?
>>
>> AnnBuilder does not make any decision on who gets mapped and who does
not. I
>> will have to step through the mapping process to tell you what might
be the
>> problem. Could you give me a few of the probes that are missed again?
>>
>> Thanks.
>>
>>
>>
>>>Regards,
>>>Hilmar
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>Search the archives:
>>
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> Jianhua Zhang
>> Department of Medical Oncology
>> Dana-Farber Cancer Institute
>> 44 Binney Street
>> Boston, MA 02115-6084
>>
>
>--
>
>Hilmar Berger
>Studienkoordinator
>Institut f?r medizinische Informatik, Statistik und Epidemiologie
>Universit?t Leipzig
>H?rtelstr. 16-18
>D-04107 Leipzig
>
>Tel. +49 341 97 16 101
>Fax. +49 341 97 16 109
>email: hilmar.berger at imise.uni-leipzig.de
Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
------------------------------
Message: 12
Date: Fri, 21 Jul 2006 15:46:03 -0600
From: "Nayeem Quayum" <nayeemquayum at gmail.com>
Subject: [BioC] Problem regardign ReadAffy()
To: bioconductor at stat.math.ethz.ch
Message-ID:
<af6d2ccc0607211446r5bb31dcj9794bbf2eb887d28 at mail.gmail.com>
Content-Type: text/plain
Hello everybody,
I was trying to load HGU133 data set in to bioconductor for some
analysis. But I got an error. Any kind of help would be appreciated. The
code is very simple
library(affy)
Data <- ReadAffy()
I invoked R from the directory where all the CEL files are resided. But
I am
getting the following error.
Error in initialize(value, ...) : Cel file /home/dev/Desktop/temp/INF
alpha/Exo_A_U133B.CEL does not seem to be of HG-U133A type
Thanks.
[[alternative HTML version deleted]]
------------------------------
Message: 13
Date: Fri, 21 Jul 2006 22:57:41 +0000 (UTC)
From: Nianhua Li <nli at fhcrc.org>
Subject: Re: [BioC] Missing chromosomal locations in hgu133a package
To: bioconductor at stat.math.ethz.ch
Message-ID: <loom.20060722T005043-363 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii
> 2. The base file used to build the annotation package may not be in
sync with
> the current probe-GB mapping provided by AffyMetrix. Nianhua, do you
know if a
> fresh download from AffyMetrix was used for release 1.8?
>
The probe-GB mapping from Affymetrix that was used for release 1.8 was
dated
Dec. 19, 2005. Six files were used to get unified probe to Entrez Gene
mapping:
1. probe-GB mapping from Affymetrix
2. probe-UniGene mapping from Affymetrix
3. probe-Entrez Gene mapping from Affymetrix
4. probe-Entrez Gene mapping from DCHIP
5. probe-Entrez Gene mapping from U. Michigan
6. probe-Entrez Gene mapping from another source (EA)
1 is the primary source, and 2-6 are supplimental sources. 1-3 are all
dated Dec
19, 2005. 4-6 are pretty old files (>1 years old).
thanks
nianhua
------------------------------
Message: 14
Date: Fri, 21 Jul 2006 23:37:56 +0000
From: "Eric J. Kort" <eric.kort at exsilico.biz>
Subject: Re: [BioC] ABPackageBuilder not building GO package?
To: "Nianhua Li" <nli at fhcrc.org>, bioconductor at stat.math.ethz.ch
Message-ID: <W2504525311296351153525076 at webmail8>
Content-Type: text/plain; charset="us-ascii"
Hi Nianhua.
No...the syntax you suggested resulted in the same set of annotation
objects being built, with no GO annotation.
Any other thoughts?
Thanks,
-Eric
>From: Nianhua Li [mailto:nli at fhcrc.org]
>Sent: Friday, July 21, 2006 12:09 PM
>To: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] ABPackageBuilder not building GO package?
>
>Hi, Eric,
>
>The "error" messages about KEGG urls are not really errors, so you can
ignore
>them. And the information about removing datasets are normal messages
as well.
>Could you please try:
>
>ABPkgBuilder(baseName="keyp.txt", baseMapType="gb", pkgName="vaimm06",
>pkgPath="./", organism="Mus musculus", version="0.1",
author=list(author="Eric
>J. Kort", maintainer="Eric J. Kort"))
>
>It is the same as your code except that "srcUrls" is removed. Let me
know if it
>doesn't work
>
>thanks
>
>Nianhua Li
>Computational Biology, PHS, FHCRC
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
------------------------------
Message: 15
Date: Fri, 21 Jul 2006 18:33:26 -0700
From: Nianhua Li <nli at fhcrc.org>
Subject: Re: [BioC] ABPackageBuilder not building GO package?
To: "Eric J. Kort" <eric.kort at exsilico.biz>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <44C18066.109 at fhcrc.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi, Eric,
I used a baseFile to test the script, and got a perfectly valid package.
Maybe your base file "keyp.txt" or your network configuration have some
problem? The script I used is :
vaimm06 <- function(pkgPath, version) {
ABPkgBuilder(baseName="mouse4302.GeneBankID",
baseMapType="gb",
pkgName="vaimm06",
pkgPath=pkgPath,
organism="Mus musculus",
version=version,
author=list(authors="Eric J. Kort", maintainer="Eric J.
Kort <eric.kort at exsilico.biz>")
)
}
vaimm06(getwd(), "0.1")
And the base file "mouse4302.GeneBankID" looks like:
41484_r_at X56681
41485_at X02152
41486_at U82396
41487_at W72400
41488_at AC002394
41489_at M99435
41490_at Y00971
41491_s_at AB028944
41492_r_at AB028944
41493_at AI094610
41494_at X99802
41495_at W37606
41496_at AL050189
41497_at AI401296
41498_at AB020718
41499_at X15218
414_at X59373
41500_at AI761818
41501_at AF004849
41502_at AI523538
41503_at AB020661
41504_s_at AF055376
...
And my environment is (I don't think it is important for this problem
though):
> sessionInfo()
R version 2.4.0 Under development (unstable) (2006-05-19 r38133)
x86_64-unknown-linux-gnu
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
[7] "datasets" "base"
other attached packages:
AnnBuilder RSQLite DBI annotate XML Biobase
"1.11.4" "0.4-1" "0.1-10" "1.9.6" "0.99-8" "1.9.28"
good luck
nianhua
------------------------------
Message: 16
Date: Fri, 21 Jul 2006 21:53:41 -0400
From: Sean Davis <sdavis2 at mail.nih.gov>
Subject: [BioC] Quick illumina question
To: Bioconductor <bioconductor at stat.math.ethz.ch>
Message-ID: <C0E6FD65.162F%sdavis2 at mail.nih.gov>
Content-Type: text/plain; charset="US-ASCII"
I have been looking at some raw illumina data. The results are reported
with the illumicode id. I can't seem to find where I can convert the
illumicode to the actual associated sequence. Can someone who is using
illumina arrays point me in the right direction?
Thanks,
Sean
------------------------------
Message: 17
Date: Sat, 22 Jul 2006 08:32:02 +0200
From: "Oosting, J. \(PATH\)" <J.Oosting at lumc.nl>
Subject: Re: [BioC] Quick illumina question
To: "Sean Davis" <sdavis2 at mail.nih.gov>, "Bioconductor"
<bioconductor at stat.math.ethz.ch>
Message-ID:
<40964D91251A18469CB08B6E96FB30BA0EF7EF at mailc.lumcnet.prod.intern>
Content-Type: text/plain
Hi Sean,
For the Golden Gate SNP arrays, Illumina delivers you .opa files that
contain annotations and which can be used to connect IllumiCode to other
variables. I have no experience with the other type of arrays, but I
guess that should be about the same.
Jan
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Sean Davis
Sent: Sat 22-Jul-06 3:53 AM
To: Bioconductor
Subject: [BioC] Quick illumina question
I have been looking at some raw illumina data. The results are reported
with the illumicode id. I can't seem to find where I can convert the
illumicode to the actual associated sequence. Can someone who is using
illumina arrays point me in the right direction?
Thanks,
Sean
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