[BioC] superpc - 'group' and 'Cox score'
Liu, Xin
Xin.Liu at arradx.com
Thu Sep 23 14:52:10 CEST 2004
Dear all,
1) When we use the package superpc, we run the code got from the tutorial. However, we got the following:
"Warning message:
Missing values for 'group' in: rowsum.default(t(x), oo)"
What did we miss?
2) 'Cox score' is very important in this package. However, I cann't find lots of information about it from web though there is lots for 'Cox regression'. Is there any other name for 'Cox score'? What is it?
Thanks a lot!
Xin LIU
-----Original Message-----
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Today's Topics:
1. Metadata for Atgenome1 array (andy phillips (RRes-Roth))
2. RE: Advice on print-tip normalization (Reimers, Mark (NIH/NCI))
3. Regarding Rgraphviz compilation error (Saurin Jani)
4. Re: Regarding Rgraphviz compilation error (Jeff Gentry)
5. Re: Regarding Rgraphviz compilation error (Saurin Jani)
6. Re: Regarding Rgraphviz compilation error (Jeff Gentry)
7. Re: Fw: [BioC] Affy Bioconductor with Rat230_2 chips
(Ali A. Pirani)
8. Re: mas5calls error with YG_S98 CEL files (Bruz Marzolf)
9. Rgraphviz Error : Rgraphviz.c: In function
`Rgraphviz_agopen': (Saurin Jani)
10. Weight functions for Agilent chips (limma) (Malard, Joel M)
11. Re: RE: Advice on print-tip normalization (Gordon K Smyth)
12. Problem with gls.series in limma (Fangxin Hong)
13. limma & targets (Giovanni Coppola)
14. Re: Weight functions for Agilent chips (limma) (Giovanni Coppola)
15. Re: Problem with gls.series in limma (Gordon Smyth)
16. Fwd: Re: [BioC] Problem with gls.series in limma (Gordon Smyth)
17. Re: limma & targets (Gordon Smyth)
18. Re: RE: Advice on print-tip normalization (Ramon Diaz-Uriarte)
----------------------------------------------------------------------
Message: 1
Date: Wed, 22 Sep 2004 12:54:26 +0100
From: "andy phillips (RRes-Roth)" <andy.phillips at bbsrc.ac.uk>
Subject: [BioC] Metadata for Atgenome1 array
To: <bioconductor at stat.math.ethz.ch>
Message-ID:
<EFDAAE7F4B83D243868A2F25AD8A4B382C1449 at rothe2ksrv1.rothamsted.bbsrc.ac.uk>
Content-Type: text/plain; charset="us-ascii"
I'm a beginner just starting with Bioconductor, and I'm having problems:
I have some old data from the Atgenome1 (8k) array that I'd like to run
through gcrma. I've installed the cdf and probe packages from the
Metadata page, but this have different names ('agcdf' and
'atgenome1probe', respectively). If I attempt to run gcrma on my CEL
data I'm told that I need 'agprobe' installed. I could try to make the
probe package myself but I can't find the appropriate probe sequence
file on the Affymetrix website.
Any ideas appreciated.
Andy Phillips
------------------------------------------------------------------------
Dr. Andy Phillips
Rothamsted Research*
Harpenden
Hertfordshire
AL5 2JQ
United Kingdom
Email : andy.phillips at bbsrc.ac.uk
Phone : +44-(0)1582-763133 ex 2801
Fax : +44-(0)1582-763010
Mobile: +44-(0)778-6066108
------------------------------------------------------------------------
*Rothamsted Research is a company limited by guarantee, registered
in England under the registration number 2393175 and a not for profit
charity number 802038.
------------------------------
Message: 2
Date: Wed, 22 Sep 2004 09:11:18 -0400
From: "Reimers, Mark (NIH/NCI)" <reimersm at mail.nih.gov>
Subject: [BioC] RE: Advice on print-tip normalization
To: bioconductor at stat.math.ethz.ch, "'gcutler at amgen.com'"
<gcutler at amgen.com>
Message-ID:
<16A0583FB1644E4DB8C0A0265028B6FD93044D at nihexchange13.nih.gov>
Content-Type: text/plain
Hello Gene,
I don't have any advice but some related observations based on looking at
regional biases on spotted microarrays. In the slide data that have come in,
there seems often to be a bias toward red on the top and bottom edges of the
print-tip groups, and a bias toward green in the middle of the print-tip
blocks. No explanation occurs to me, but this effect is apparent on most of
the arrays. One of our collaborators claims the effect disappears with a
more effective washing treatment, but hasn't sent slide images.
Such an effect ought to produce the periodicity you comment on below.
Has any one else noticed a similar phenomenon?
Regards
Mark
Date: Fri, 17 Sep 2004 10:32:33 -0700
From: Gene Cutler <gcutler at amgen.com>
Subject: [BioC] Advice on print-tip normalization
To: bioconductor at stat.math.ethz.ch
Message-ID: <8EC0413E-08CF-11D9-95E4-000A95C91324 at amgen.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hello. I've just started using the marray package for processing a set
of spotted oligo arrays. The arrays, when intensities or log ratios
are plotted against probe number, show a clear pattern of
rising/falling values with a periodicity equal to the grid block size
(~3600 spots). I can see a similar periodicity in the printTip
boxplots generated with marray. Running printTipLoess smoothes out the
boxplot nicely (and the MA plot also looks much nicer), but,
surprisingly, when I export the normalized values and plot them against
position, the grid block periodicity is little changed.
I've tried different span values for the printTipLoess as well as
trying with or without scaling (e.g. printTipMAD), but nothing I do
seems to have much effect on this data artifact.
Does anyone have any suggestions?
Thanks.
--
Gene Cutler
Research Investigator
Bioinformatics
Amgen SF
Mark Reimers,
senior research fellow,
National Cancer Inst., and SRA,
9000 Rockville Pike, bldg 37, room 5068
Bethesda MD 20892
[[alternative HTML version deleted]]
------------------------------
Message: 3
Date: Wed, 22 Sep 2004 09:39:11 -0700 (PDT)
From: Saurin Jani <saurin_jani at yahoo.com>
Subject: [BioC] Regarding Rgraphviz compilation error
To: bioconductor at stat.math.ethz.ch
Message-ID: <20040922163912.16917.qmail at web41115.mail.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Hi BioC,
I have problem installing Rgraphviz on my Linux
Fedora 2 with 32bit AMD Athlon with 512 RAM
login as me: (not as root)
I have installed latest graphviz :
graphviz-1.16-1.src.rpm
$whereis graphviz
graphviz: /usr/lib/graphviz /usr/include/graphviz
/usr/share/graphviz
if do:
R CMD INSTALL -l /usr/local/lib/R/library
Rgraphviz_1.4.23.tar.gz
get get:
ERROR: compilation failed for package 'Rgraphviz'
If someone has problem like this and solved , please
let me know.
Thank you,
Saurin
------------------------------
Message: 4
Date: Wed, 22 Sep 2004 12:54:01 -0400 (EDT)
From: Jeff Gentry <jgentry at jimmy.harvard.edu>
Subject: Re: [BioC] Regarding Rgraphviz compilation error
To: Saurin Jani <saurin_jani at yahoo.com>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.SOL.4.20.0409221253410.27420-100000 at santiam.dfci.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> R CMD INSTALL -l /usr/local/lib/R/library
> Rgraphviz_1.4.23.tar.gz
>
> get get:
> ERROR: compilation failed for package 'Rgraphviz'
Would you like to include just a *little* more of the output?
Thanks
-J
------------------------------
Message: 5
Date: Wed, 22 Sep 2004 10:11:16 -0700 (PDT)
From: Saurin Jani <saurin_jani at yahoo.com>
Subject: Re: [BioC] Regarding Rgraphviz compilation error
To: Jeff Gentry <jgentry at jimmy.harvard.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <20040922171116.6335.qmail at web41112.mail.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Hi Jeff,
More output of Rgraphviz compilation error:
$ R CMD INSTALL -l /usr/local/lib/R/library
Rgraphviz_1.4.23.tar.gz
I get : --------------------------------
* Installing *source* package 'Rgraphviz' ...
checking for graphviz... checking for
dotneato-config... /usr/bin/dotneato-config
/usr/bin/dotneato-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include -I/usr/include/graphviz
-DGRAPHVIZ_1_12 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c
Rgraphviz.c -o Rgraphviz.o
In file included from
/usr/include/graphviz/render.h:49,
from common.h:22,
from Rgraphviz.c:1:
/usr/include/graphviz/macros.h:28:1: warning: "NEW"
redefined
In file included from common.h:13,
from Rgraphviz.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
In file included from
/usr/include/graphviz/types.h:11,
from
/usr/include/graphviz/render.h:51,
from common.h:22,
from Rgraphviz.c:1:
/usr/include/graphviz/pathplan.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/pathplan.h:16,
from
/usr/include/graphviz/types.h:11,
from
/usr/include/graphviz/render.h:51,
from common.h:22,
from Rgraphviz.c:1:
/usr/include/graphviz/pathgeom.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:52,
from common.h:22,
from Rgraphviz.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:55,
from common.h:22,
from Rgraphviz.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/gvrender.h:19,
from
/usr/include/graphviz/render.h:55,
from common.h:22,
from Rgraphviz.c:1:
/usr/include/graphviz/gvrenderint.h:12: warning:
ignoring #pragma prototyped
In file included from common.h:23,
from Rgraphviz.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:26,
from Rgraphviz.c:1:
/usr/include/graphviz/adjust.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:28,
from Rgraphviz.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
gcc -I/usr/local/lib/R/include -I/usr/include/graphviz
-DGRAPHVIZ_1_12 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c
RgraphvizInit.c -o RgraphvizInit.o
In file included from
/usr/include/graphviz/render.h:49,
from common.h:22,
from RgraphvizInit.c:1:
/usr/include/graphviz/macros.h:28:1: warning: "NEW"
redefined
In file included from common.h:13,
from RgraphvizInit.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
In file included from
/usr/include/graphviz/types.h:11,
from
/usr/include/graphviz/render.h:51,
from common.h:22,
from RgraphvizInit.c:1:
/usr/include/graphviz/pathplan.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/pathplan.h:16,
from
/usr/include/graphviz/types.h:11,
from
/usr/include/graphviz/render.h:51,
from common.h:22,
from RgraphvizInit.c:1:
/usr/include/graphviz/pathgeom.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:52,
from common.h:22,
from RgraphvizInit.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:55,
from common.h:22,
from RgraphvizInit.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/gvrender.h:19,
from
/usr/include/graphviz/render.h:55,
from common.h:22,
from RgraphvizInit.c:1:
/usr/include/graphviz/gvrenderint.h:12: warning:
ignoring #pragma prototyped
In file included from common.h:23,
from RgraphvizInit.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:26,
from RgraphvizInit.c:1:
/usr/include/graphviz/adjust.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:28,
from RgraphvizInit.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
common.h:33: warning: `gvc' defined but not used
gcc -shared -L/usr/local/lib -o Rgraphviz.so
Rgraphviz.o RgraphvizInit.o -Wl -L/usr/lib/graphviz
-ldotneato -lm
/usr/bin/ld: cannot find -ldotneato
collect2: ld returned 1 exit status
make: *** [Rgraphviz.so] Error 1
ERROR: compilation failed for package 'Rgraphviz'
** Removing '/usr/local/lib/R/library/Rgraphviz'
---------------------------------------------
Please let me know...
Thank you,
Saurin
--- Jeff Gentry <jgentry at jimmy.harvard.edu> wrote:
> > R CMD INSTALL -l /usr/local/lib/R/library
> > Rgraphviz_1.4.23.tar.gz
> >
> > get get:
> > ERROR: compilation failed for package 'Rgraphviz'
>
> Would you like to include just a *little* more of
> the output?
>
> Thanks
> -J
>
>
_______________________________
Declare Yourself - Register online to vote today!
------------------------------
Message: 6
Date: Wed, 22 Sep 2004 13:16:34 -0400 (EDT)
From: Jeff Gentry <jgentry at jimmy.harvard.edu>
Subject: Re: [BioC] Regarding Rgraphviz compilation error
To: Saurin Jani <saurin_jani at yahoo.com>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
<Pine.SOL.4.20.0409221316060.27420-100000 at santiam.dfci.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> /usr/bin/ld: cannot find -ldotneato
> collect2: ld returned 1 exit status
include the graphviz library dir (e.g. /usr/local/lib/graphviz) in your
LD_LIBRARY_PATH.
------------------------------
Message: 7
Date: Wed, 22 Sep 2004 12:58:57 -0400
From: "Ali A. Pirani" <aapiran at LearnLink.Emory.Edu>
Subject: Re: Fw: [BioC] Affy Bioconductor with Rat230_2 chips
To: bioconductor at stat.math.ethz.ch
Message-ID:
<fc.00249f0f212715f33b9aca007b8705de.2127163b at LearnLink.Emory.Edu>
Content-Type: text/plain; charset=ISO-8859-1
Dear Crispin (or anybody),
According to your message, the new version of simpleaffy will fix this error,
but we seem to sill be encountering it. Is the latest version of simpleaffy
1.3.2 found on this page:
http://bioconductor.org/repository/devel/package/html/simpleaffy.html
?
Any assistance will be appreciated, because even though we updated all of our
installations, we still see the below error message.
Thanks,
Ali
BIMCORE
"Kim Gernert" <gernert at emory.edu> on Wednesday, May 05, 2004 at 2:37 PM -0500
wrote:
>
>Kim M. Gernert
>Director BimCore
>mail: 4001 Rollins Research Ctr
>loc: G236 Biochem. Connector
>Emory University
>Atlanta, GA 30322
>ph 404-727-3501
>fax 404-727-5512
>----- Original Message -----
>From: "Crispin Miller" <CMiller at PICR.man.ac.uk>
>To: "Kim Gernert" <gernert at emory.edu>
>Cc: <bioconductor at stat.math.ethz.ch>
>Sent: Monday, April 26, 2004 2:57 AM
>Subject: RE: [BioC] Affy Bioconductor with Rat230_2 chips
>
>
>> Hi Kim,
>> The new version of simpleaffy has a lot of bug fixes and stuff in it, so
>> I'd suggest using it anyway... ;-)
>>
>> The qc.stats code needs to know which chip you're using, to pick the
>> right spike probes - and detection p-value stuff needs to use it to work
>> out which alpha1 and alpha2 parameters to use...
>> I'm going to modify the code so you can specify the probes you wish to
>> use and stuff like that. In the next day or two I'll add the rat2302cdf
>> to the lists and upload a new version...
>> Cheers,
>> Crispin
>>
>>
>> -----Original Message-----
>> From: bioconductor-bounces at stat.math.ethz.ch
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Kim Gernert
>> Sent: 23 April 2004 20:35
>> To: bioconductor at stat.math.ethz.ch
>> Subject: [BioC] Affy Bioconductor with Rat230_2 chips
>>
>>
>>
>> I am trying to process Affymetrix array data from the new rat chip
>> (RAT230_2). We followed the vignette on setting up the new rat230-2.cdf
>> file and all seemed
>> fine (readaffy, rnadeg..., rma, etc.) until I tried
>>
>> (simpleaffy) qc.stats
>>
>> ERROR: I am sorry I donot know spike probes on rat230.2.cdf
>>
>>
>> Do I need the new simpleaffy (last download Mar 2004), do I need the new
>> R (currently running 1.8.1, on Linux)? or is there an additional script
>> I need to run to inform R of the new parameters
>> (spikes, etc.) for the RAT230_2?
>>
>>
>> Your help is appreciated.
>>
>> Kim M. Gernert
>>
>>
>>
>>
>> ---
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>>
>> --------------------------------------------------------
>>
>>
>> This email is confidential and intended solely for the use of the
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>opinions presented are solely those of the author and do not necessarily
>represent those of the Paterson Institute for Cancer Research or the
>Christie Hospital NHS Trust. It may contain information that is privileged &
>confidential within the meaning of applicable law. Accordingly any
>dissemination, distribution, copying, or other use of this message, or any
>of its contents, by any person other than the intended recipient may
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>you are NOT the intended recipient please contact the sender and dispose of
>this e-mail as soon as possible.
>>
>>
>
>
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>
------------------------------
Message: 8
Date: Wed, 22 Sep 2004 12:02:24 -0700
From: "Bruz Marzolf" <bmarzolf at systemsbiology.org>
Subject: Re: [BioC] mas5calls error with YG_S98 CEL files
To: <bioconductor at stat.math.ethz.ch>
Message-ID:
<BFBA7186C5B3CB4C8EA0B509FA9090B304EB04 at exchange.systemsbiology.net>
Content-Type: text/plain; charset="iso-8859-1"
Upon further investigation, it appears that failure of mas5calls to work with YG_S98 chips is due to these yeast chips containing probe sets which only have 1 probe pair each. Curious about how GCOS handles these probe sets, I checked and it appears that probe sets with 1 probe pair always receive a p-value of either 0.25 or 0.75.
Could a solution/work-around for this problem be implemented? I'm guessing that the person who originally wrote the code will have the best idea of how this 1 probe pair scenario ought to be dealt with.
Best wishes,
Bruz
> Date: Mon, 20 Sep 2004 14:34:38 -0700
> From: "Bruz Marzolf" <bmarzolf at systemsbiology.org>
> Subject: [BioC] mas5calls error with YG_S98 CEL files
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID:
>
> <BFBA7186C5B3CB4C8EA0B509FA9090B304EB01 at exchange.systemsbiology.net>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
> I've encountered trouble when using mas5calls on CEL files
> from YG_S98 chips:
>
> data <- ReadAffy(filenames = cel.file.name)
> PACalls <- mas5calls(data)
>
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in if (y < alpha1) { : missing value where
> TRUE/FALSE needed
>
> Both the release and developmental version of the 'affy'
> package produce this same error, but only with YG_S98 chips
> (same code works fine on HG-U133_Plus_2 or Mouse430_2 chips).
> Has anyone encountered this before?
>
> Thanks!
> Bruz
------------------------------
Message: 9
Date: Wed, 22 Sep 2004 13:17:14 -0700 (PDT)
From: Saurin Jani <saurin_jani at yahoo.com>
Subject: [BioC] Rgraphviz Error : Rgraphviz.c: In function
`Rgraphviz_agopen':
To: "'BioConductor mailing list'" <bioconductor at stat.math.ethz.ch>
Message-ID: <20040922201714.58656.qmail at web41126.mail.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Hi,
I have error in Rgraphviz installation. I have latest
graphviz-1.16.tar.gz installed.
System: Linux Fedora core 2 - AMD 32 Bit - 512 RAM
$ R CMD INSTALL -l /usr/local/lib/R/library
Rgraphviz_1.4.0.tar.gz
I am getting...
--------------------------------------------
* Installing *source* package 'Rgraphviz' ...
** libs
gcc -I/usr/local/lib/R/include `dotneato-config
--cflags` -I/usr/local/include -D__NO_MATH_INLINES
-mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o
Rgraphviz.o
In file included from
/usr/local/include/graphviz/render.h:45,
from common.h:21,
from Rgraphviz.c:1:
/usr/local/include/graphviz/macros.h:34:1: warning:
"NEW" redefined
In file included from common.h:13,
from Rgraphviz.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
Rgraphviz.c: In function `Rgraphviz_agopen':
Rgraphviz.c:244: warning: implicit declaration of
function `GD_gvc'
Rgraphviz.c:244: error: invalid lvalue in assignment
make: *** [Rgraphviz.o] Error 1
ERROR: compilation failed for package 'Rgraphviz'
** Removing '/usr/local/lib/R/library/Rgraphviz'
-------------------
please, let me know if someone has already solved this
error.
thanks,
Saurin
------------------------------
Message: 10
Date: Wed, 22 Sep 2004 14:56:28 -0700
From: "Malard, Joel M" <JM.Malard at pnl.gov>
Subject: [BioC] Weight functions for Agilent chips (limma)
To: bioconductor at stat.math.ethz.ch
Message-ID: <AF293AF0A07C8A44A6098DA99D0371309C3DBD at pnlmse24.pnl.gov>
Content-Type: text/plain
Dear All,
I was wondering what other people have been using for the weight
function in read.maimages with Agilent arrays? I tried the following:
wtAgilent.GFilter <- function(qta) { qta[,"gIsPosAndSignif"] }
wtAgilent.RGFilter <- function(qta) {
(qta[,"rIsPosAndSignif"]+qta[,"gIsPosAndSignif"])/2.0 }
wtAgilent.RFilter <- function(qta) { qta[,"rIsPosAndSignif"] }
wtAgilent.mRGFilter <- function(qta) {
mapply(min,qta[,"gIsPosAndSignif"],qta[,"rIsPosAndSignif"]) }
The last one seems to give somewhat "better results by-eye" when
followed by loess normalization but is rather subjective.
Best regards,
Joel Malard
> -----Original Message-----
> From: Malard, Joel M
> Sent: Friday, September 17, 2004 12:44 PM
> To: 'bioconductor at stat.math.ethz.ch'
> Subject: Loess normalization for Agilent chips
>
>
> I am struggling to get data from Agilent cDNA arrays into
> BioConductor. It seems to me much easier to get the data in affy's
> normalize.loess() than in the other cDNA array packages.
>
> Given that "one who get a bargain get what he pays for", does anyone
> has comments, recommendations or warnings to share about using an Affy
> normalization procedure on cDNA data?
>
> Thanks,
>
> Joel M. Malard, Ph.D.
> Scientist IV
> Pacific Northwest National Laboratory
> Battelle Boulevard, PO Box 999
> Mail Stop K1-85
> Richland, WA 99352
>
> "I love the audacity of those who have everything to loose from it;
> the moderation of those who have nothing to gain from it." Rostand,
> Jean (1894-1977)
>
>
[[alternative HTML version deleted]]
------------------------------
Message: 11
Date: Thu, 23 Sep 2004 08:36:28 +1000 (EST)
From: "Gordon K Smyth" <smyth at wehi.EDU.AU>
Subject: Re: [BioC] RE: Advice on print-tip normalization
To: "Reimers, Mark (NIH/NCI)" <reimersm at mail.nih.gov>
Cc: "'gcutler at amgen.com'" <gcutler at amgen.com>,
bioconductor at stat.math.ethz.ch
Message-ID: <2254.211.31.120.140.1095892588.squirrel at 211.31.120.140>
Content-Type: text/plain;charset=iso-8859-1
Spots in a given position within a print-tip group are always printed from
the same 384-well plate of DNA. Genes of similar function or homology
are often grouped together on a plate. If there are systematic differences
between plates due to the nature of the probes, this would lead to periodicity
through the print-tip groups, but you certainly don't want
to remove this structure in the normalization.
Gordon
> Hello Gene,
> I don't have any advice but some related observations based on looking at
> regional biases on spotted microarrays. In the slide data that have come in,
> there seems often to be a bias toward red on the top and bottom edges of the
> print-tip groups, and a bias toward green in the middle of the print-tip
> blocks. No explanation occurs to me, but this effect is apparent on most of
> the arrays. One of our collaborators claims the effect disappears with a
> more effective washing treatment, but hasn't sent slide images.
>
> Such an effect ought to produce the periodicity you comment on below.
>
> Has any one else noticed a similar phenomenon?
>
>
> Regards
>
> Mark
>
>
> Date: Fri, 17 Sep 2004 10:32:33 -0700
> From: Gene Cutler <gcutler at amgen.com>
> Subject: [BioC] Advice on print-tip normalization
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <8EC0413E-08CF-11D9-95E4-000A95C91324 at amgen.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hello. I've just started using the marray package for processing a set
> of spotted oligo arrays. The arrays, when intensities or log ratios
> are plotted against probe number, show a clear pattern of
> rising/falling values with a periodicity equal to the grid block size
> (~3600 spots). I can see a similar periodicity in the printTip
> boxplots generated with marray. Running printTipLoess smoothes out the
> boxplot nicely (and the MA plot also looks much nicer), but,
> surprisingly, when I export the normalized values and plot them against
> position, the grid block periodicity is little changed.
>
> I've tried different span values for the printTipLoess as well as
> trying with or without scaling (e.g. printTipMAD), but nothing I do
> seems to have much effect on this data artifact.
>
> Does anyone have any suggestions?
>
> Thanks.
>
> --
> Gene Cutler
> Research Investigator
> Bioinformatics
> Amgen SF
>
>
>
> Mark Reimers,
> senior research fellow,
> National Cancer Inst., and SRA,
> 9000 Rockville Pike, bldg 37, room 5068
> Bethesda MD 20892
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
------------------------------
Message: 12
Date: Wed, 22 Sep 2004 16:52:55 -0700 (PDT)
From: "Fangxin Hong" <fhong at salk.edu>
Subject: [BioC] Problem with gls.series in limma
To: bioconductor at stat.math.ethz.ch
Message-ID: <2371.10.10.200.247.1095897175.squirrel at 10.10.200.247>
Content-Type: text/plain;charset=iso-8859-1
Hi there;
I tried to use gls.series to get least square fit for each gene, but I
got the following error message:
--------------------------------------------------
Loading required package: statmod
Attaching package 'statmod':
The following object(s) are masked from package:limma :
matvec vecmat
Error in randomizedBlockFit(y, X, Z, fixed.estimates = FALSE) :
unused argument(s) (fixed.estimates ...)
------------------------------------------------------
Any clue?
Thanks a lot!
fangxin
--
Fangxin Hong, Ph.D.
Bioinformatics Specialist
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
------------------------------
Message: 13
Date: Wed, 22 Sep 2004 17:02:53 -0700
From: Giovanni Coppola <gcoppola at ucla.edu>
Subject: [BioC] limma & targets
To: bioconductor at stat.math.ethz.ch
Message-ID: <6.1.2.0.2.20040922161857.0415ba00 at mail.ucla.edu>
Content-Type: text/plain
I am analyzing 12 Agilent slides with LIMMA (ver 1.7.7, R: 1.9.1)
I load my targets file with this line...
targets<-readTargets(file="targets.txt", path = "C:/Documents and
Settings/giovanni/analysis")
... and I read the data with this line:
RG <-read.maimages(name=targets$Name,source="agilent", ext="txt", path =
"C:/Documents and Settings/giovanni/analysis/data",verbose=TRUE,
wt.fun=mywtfun(c(1)))
Now, if I type 'targets' I obtain (as expected) the following:
slide.number Name
FileName cy5 cy3
jc_251197823988_S01_A01 1
e6-c3h jc_251197823988_S01_A01.txt e c
jc_16011978013880_S01_A01 2 c3-e6h
jc_16011978013880_S01_A01.txt c e
jc_16011978013882_S01_A01 3 e4-c7h
jc_16011978013882_S01_A01.txt e c
jc_16011978013881_S01_A01 4 c7-e4h
jc_16011978013881_S01_A01.txt c e
jc_251197823979_S01_A01 5
e7-c8h jc_251197823979_S01_A01.txt e c
jc_251197823980_S01_A01 6
c8-e7h jc_251197823980_S01_A01.txt c e
jc_251197823977_S01_A01 7
e6-c3m jc_251197823977_S01_A01.txt e c
jc_251197823978_S01_A01 8
c3-e6m jc_251197823978_S01_A01.txt c e
jc_251197823989_S01_A01 9
e3-c4m jc_251197823989_S01_A01.txt e c
jc_251197823990_S01_A01 10
c4-e3m jc_251197823990_S01_A01.txt c e
jc_251197824015_S01_A01 11
e7-c8m jc_251197824015_S01_A01.txt e c
jc_251197824017_S01_A01 12
c8-e7m jc_251197824017_S01_A01.txt c e
But, if I type 'RG$targets' I get this:
e6-c3h jc_16011978013880_S01_A01
c3-e6h jc_16011978013881_S01_A01
e4-c7h jc_16011978013882_S01_A01
c7-e4h jc_251197823977_S01_A01
e7-c8h jc_251197823978_S01_A01
c8-e7h jc_251197823979_S01_A01
e6-c3m jc_251197823980_S01_A01
c3-e6m jc_251197823988_S01_A01
e3-c4m jc_251197823989_S01_A01
c4-e3m jc_251197823990_S01_A01
e7-c8m jc_251197824015_S01_A01
c8-e7m jc_251197824017_S01_A01
So, the slide RG[,2] points to the file 'jc_16011978013881_S01_A01', and
has a mismatched name ('c3-e6h')!!
If I try (not specifying name=)
RG <-read.maimages(source="agilent", ext="txt", path = "C:/Documents and
Settings/giovanni/analysis/data",verbose=TRUE, wt.fun=mywtfun(c(1)))
...RG[,2] has no name, but the file ('jc_16011978013881_S01_A01') is still
not corresponding to the slide #2 in targets.txt.
It looks like read.maimages sorted the files in alphabetical
order....without touching the slide names...
I can change the file names, but I wonder if I made any mistakes, or this
is a point to look at.
Thanks
Giovanni
[[alternative HTML version deleted]]
------------------------------
Message: 14
Date: Wed, 22 Sep 2004 17:20:11 -0700
From: Giovanni Coppola <gcoppola at ucla.edu>
Subject: Re: [BioC] Weight functions for Agilent chips (limma)
To: "Malard, Joel M" <JM.Malard at pnl.gov>,
bioconductor at stat.math.ethz.ch
Message-ID: <6.1.2.0.2.20040922170340.040c1a98 at mail.ucla.edu>
Content-Type: text/plain
Hi Joel,
actually, I was trying to use the 8 outlier fields (columns AZ-BG of the
Agilent output file) in a way similar to the 'flag' fields of other platfoms...
So, I started with
mywtfun <- function(exclude.flags=c(1,2,3)) function(obj)
1-(obj$rIsBGPopnOL %in% exclude.flags)
and thenRG <-read.maimages(...blabla... wt.fun=mywtfun(c(1)))
and maybe there's a way to include the other fields as well....
Any other ideas?
Cheers
Giovanni
At 02:56 PM 9/22/2004, Malard, Joel M wrote:
>Dear All,
>
>I was wondering what other people have been using for the weight
>function in read.maimages with Agilent arrays? I tried the following:
>
>wtAgilent.GFilter <- function(qta) { qta[,"gIsPosAndSignif"] }
>wtAgilent.RGFilter <- function(qta) {
>(qta[,"rIsPosAndSignif"]+qta[,"gIsPosAndSignif"])/2.0 }
>wtAgilent.RFilter <- function(qta) { qta[,"rIsPosAndSignif"] }
>wtAgilent.mRGFilter <- function(qta) {
>mapply(min,qta[,"gIsPosAndSignif"],qta[,"rIsPosAndSignif"]) }
>
>The last one seems to give somewhat "better results by-eye" when
>followed by loess normalization but is rather subjective.
>
>Best regards,
>
>Joel Malard
>
> > -----Original Message-----
> > From: Malard, Joel M
> > Sent: Friday, September 17, 2004 12:44 PM
> > To: 'bioconductor at stat.math.ethz.ch'
> > Subject: Loess normalization for Agilent chips
> >
> >
> > I am struggling to get data from Agilent cDNA arrays into
> > BioConductor. It seems to me much easier to get the data in affy's
> > normalize.loess() than in the other cDNA array packages.
> >
> > Given that "one who get a bargain get what he pays for", does anyone
> > has comments, recommendations or warnings to share about using an Affy
> > normalization procedure on cDNA data?
> >
> > Thanks,
> >
> > Joel M. Malard, Ph.D.
> > Scientist IV
> > Pacific Northwest National Laboratory
> > Battelle Boulevard, PO Box 999
> > Mail Stop K1-85
> > Richland, WA 99352
> >
> > "I love the audacity of those who have everything to loose from it;
> > the moderation of those who have nothing to gain from it." Rostand,
> > Jean (1894-1977)
> >
> >
>
> [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
[[alternative HTML version deleted]]
------------------------------
Message: 15
Date: Thu, 23 Sep 2004 10:55:07 +1000
From: Gordon Smyth <smyth at wehi.edu.au>
Subject: Re: [BioC] Problem with gls.series in limma
To: fhong at salk.edu
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <6.0.1.1.1.20040923104501.0294cce0 at imaphost.wehi.edu.au>
Content-Type: text/plain; charset="us-ascii"; format=flowed
You're using an older version of limma with a newer version of statmod.
This may have
occured because you have the last Bioconductor release of limma with a more
recent
version of statmod from CRAN. The problem is that Bioconductor updates its
packages
only once every 6 months (unless you use the developmental version, which I
don't
recommend) while CRAN packages are updated as required.
The solution is to update limma and statmod directly from CRAN, which will give
you the current versions of both packages. Just use
install.packages("limma")
or use the drop down menu if you're using Windows.
BTW, I recommend that you move to mFit() rather than using gls.series()
directly.
Gordon
At 09:52 AM 23/09/2004, Fangxin Hong wrote:
>Hi there;
> I tried to use gls.series to get least square fit for each gene, but I
>got the following error message:
>--------------------------------------------------
>Loading required package: statmod
>
>Attaching package 'statmod':
>
>
> The following object(s) are masked from package:limma :
>
> matvec vecmat
>
>Error in randomizedBlockFit(y, X, Z, fixed.estimates = FALSE) :
> unused argument(s) (fixed.estimates ...)
>------------------------------------------------------
>
>Any clue?
>
>Thanks a lot!
>
>
>fangxin
>
>
>--
>Fangxin Hong, Ph.D.
>Bioinformatics Specialist
>Plant Biology Laboratory
>The Salk Institute
>10010 N. Torrey Pines Rd.
>La Jolla, CA 92037
>E-mail: fhong at salk.edu
------------------------------
Message: 16
Date: Thu, 23 Sep 2004 11:19:18 +1000
From: Gordon Smyth <smyth at wehi.edu.au>
Subject: Fwd: Re: [BioC] Problem with gls.series in limma
To: fhong at salk.edu
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <6.0.1.1.1.20040923110558.0295bb70 at imaphost.wehi.edu.au>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Actually on checking back through the records, I can see that none of the
Bioconductor
release versions of limma would have given the below error. You must be
using an
in-between version of limma from between Feb 8 and March 20 of this year
with a later version (after March 20) of statmod.
As an Bioinformatics Specialist, I'm sure you will appreciate that it is a
good idea
to quote the version number of software that you're asking questions about,
and that
it is a good idea to try updating to current software to see if it solves
your problem.
Gordon
>Date: Thu, 23 Sep 2004 10:55:07 +1000
>To: fhong at salk.edu
>From: Gordon Smyth <smyth at wehi.edu.au>
>Subject: Re: [BioC] Problem with gls.series in limma
>Cc: bioconductor at stat.math.ethz.ch
>
>You're using an older version of limma with a newer version of statmod.
>This may have
>occured because you have the last Bioconductor release of limma with a
>more recent
>version of statmod from CRAN. The problem is that Bioconductor updates its
>packages
>only once every 6 months (unless you use the developmental version, which
>I don't
>recommend) while CRAN packages are updated as required.
>
>The solution is to update limma and statmod directly from CRAN, which will
>give
>you the current versions of both packages. Just use
>
> install.packages("limma")
>
>or use the drop down menu if you're using Windows.
>
>BTW, I recommend that you move to mFit() rather than using gls.series()
>directly.
>
>Gordon
>
>At 09:52 AM 23/09/2004, Fangxin Hong wrote:
>>Hi there;
>> I tried to use gls.series to get least square fit for each gene, but I
>>got the following error message:
>>--------------------------------------------------
>>Loading required package: statmod
>>
>>Attaching package 'statmod':
>>
>>
>> The following object(s) are masked from package:limma :
>>
>> matvec vecmat
>>
>>Error in randomizedBlockFit(y, X, Z, fixed.estimates = FALSE) :
>> unused argument(s) (fixed.estimates ...)
>>------------------------------------------------------
>>
>>Any clue?
>>
>>Thanks a lot!
>>
>>
>>fangxin
>>
>>
>>--
>>Fangxin Hong, Ph.D.
>>Bioinformatics Specialist
>>Plant Biology Laboratory
>>The Salk Institute
>>10010 N. Torrey Pines Rd.
>>La Jolla, CA 92037
>>E-mail: fhong at salk.edu
------------------------------
Message: 17
Date: Thu, 23 Sep 2004 11:46:39 +1000
From: Gordon Smyth <smyth at wehi.edu.au>
Subject: Re: [BioC] limma & targets
To: Giovanni Coppola <gcoppola at ucla.edu>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <6.0.1.1.1.20040923112622.029d4e20 at imaphost.wehi.edu.au>
Content-Type: text/plain; charset="us-ascii"; format=flowed
At 10:02 AM 23/09/2004, Giovanni Coppola wrote:
>I am analyzing 12 Agilent slides with LIMMA (ver 1.7.7, R: 1.9.1)
>I load my targets file with this line...
>
>targets<-readTargets(file="targets.txt", path = "C:/Documents and
>Settings/giovanni/analysis")
>
>... and I read the data with this line:
>
>RG <-read.maimages(name=targets$Name,source="agilent", ext="txt", path =
>"C:/Documents and Settings/giovanni/analysis/data",verbose=TRUE,
>wt.fun=mywtfun(c(1)))
You need
RG <- read.maimages(files=targets$FileName, etc
If you don't specify 'files', then all the '.ext' files will be read in
alphabetical
order.
If you specify 'names' but not 'files', as you have done, you risk random
association of names with files.
Gordon
>Now, if I type 'targets' I obtain (as expected) the following:
> slide.number Name
>FileName cy5 cy3
>jc_251197823988_S01_A01 1
>e6-c3h jc_251197823988_S01_A01.txt e c
>jc_16011978013880_S01_A01 2 c3-e6h
>jc_16011978013880_S01_A01.txt c e
>jc_16011978013882_S01_A01 3 e4-c7h
>jc_16011978013882_S01_A01.txt e c
>jc_16011978013881_S01_A01 4 c7-e4h
>jc_16011978013881_S01_A01.txt c e
>jc_251197823979_S01_A01 5
>e7-c8h jc_251197823979_S01_A01.txt e c
>jc_251197823980_S01_A01 6
>c8-e7h jc_251197823980_S01_A01.txt c e
>jc_251197823977_S01_A01 7
>e6-c3m jc_251197823977_S01_A01.txt e c
>jc_251197823978_S01_A01 8
>c3-e6m jc_251197823978_S01_A01.txt c e
>jc_251197823989_S01_A01 9
>e3-c4m jc_251197823989_S01_A01.txt e c
>jc_251197823990_S01_A01 10
>c4-e3m jc_251197823990_S01_A01.txt c e
>jc_251197824015_S01_A01 11
>e7-c8m jc_251197824015_S01_A01.txt e c
>jc_251197824017_S01_A01 12
>c8-e7m jc_251197824017_S01_A01.txt c e
>
>But, if I type 'RG$targets' I get this:
>
>e6-c3h jc_16011978013880_S01_A01
>c3-e6h jc_16011978013881_S01_A01
>e4-c7h jc_16011978013882_S01_A01
>c7-e4h jc_251197823977_S01_A01
>e7-c8h jc_251197823978_S01_A01
>c8-e7h jc_251197823979_S01_A01
>e6-c3m jc_251197823980_S01_A01
>c3-e6m jc_251197823988_S01_A01
>e3-c4m jc_251197823989_S01_A01
>c4-e3m jc_251197823990_S01_A01
>e7-c8m jc_251197824015_S01_A01
>c8-e7m jc_251197824017_S01_A01
>
>So, the slide RG[,2] points to the file 'jc_16011978013881_S01_A01', and
>has a mismatched name ('c3-e6h')!!
>
>If I try (not specifying name=)
>RG <-read.maimages(source="agilent", ext="txt", path = "C:/Documents and
>Settings/giovanni/analysis/data",verbose=TRUE, wt.fun=mywtfun(c(1)))
>
>...RG[,2] has no name, but the file ('jc_16011978013881_S01_A01') is still
>not corresponding to the slide #2 in targets.txt.
>
>It looks like read.maimages sorted the files in alphabetical
>order....without touching the slide names...
>I can change the file names, but I wonder if I made any mistakes, or this
>is a point to look at.
>
>Thanks
>Giovanni
------------------------------
Message: 18
Date: Thu, 23 Sep 2004 10:12:39 +0200
From: Ramon Diaz-Uriarte <rdiaz at cnio.es>
Subject: Re: [BioC] RE: Advice on print-tip normalization
To: bioconductor at stat.math.ethz.ch
Cc: "Reimers, Mark \(NIH/NCI\)" <reimersm at mail.nih.gov>,
"'gcutler at amgen.com'" <gcutler at amgen.com>
Message-ID: <200409231012.39555.rdiaz at cnio.es>
Content-Type: text/plain; charset="iso-8859-1"
Dear Mark and Gene,
With regards to the periodicity the "Print-order normalization of cDNA
microarrays" by Gordon Smyth
(http://www.statsci.org/smyth/pubs/porder/porder.html)
could be of interest.
I do have observed sometimes these print order effects here, and have used the
approaches suggested in Smyth's document.
Best,
R.
On Wednesday 22 September 2004 15:11, Reimers, Mark (NIH/NCI) wrote:
> Hello Gene,
> I don't have any advice but some related observations based on looking at
> regional biases on spotted microarrays. In the slide data that have come
> in, there seems often to be a bias toward red on the top and bottom edges
> of the print-tip groups, and a bias toward green in the middle of the
> print-tip blocks. No explanation occurs to me, but this effect is apparent
> on most of the arrays. One of our collaborators claims the effect
> disappears with a more effective washing treatment, but hasn't sent slide
> images.
>
> Such an effect ought to produce the periodicity you comment on below.
>
> Has any one else noticed a similar phenomenon?
>
>
> Regards
>
> Mark
>
>
> Date: Fri, 17 Sep 2004 10:32:33 -0700
> From: Gene Cutler <gcutler at amgen.com>
> Subject: [BioC] Advice on print-tip normalization
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <8EC0413E-08CF-11D9-95E4-000A95C91324 at amgen.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hello. I've just started using the marray package for processing a set
> of spotted oligo arrays. The arrays, when intensities or log ratios
> are plotted against probe number, show a clear pattern of
> rising/falling values with a periodicity equal to the grid block size
> (~3600 spots). I can see a similar periodicity in the printTip
> boxplots generated with marray. Running printTipLoess smoothes out the
> boxplot nicely (and the MA plot also looks much nicer), but,
> surprisingly, when I export the normalized values and plot them against
> position, the grid block periodicity is little changed.
>
> I've tried different span values for the printTipLoess as well as
> trying with or without scaling (e.g. printTipMAD), but nothing I do
> seems to have much effect on this data artifact.
>
> Does anyone have any suggestions?
>
> Thanks.
>
> --
> Gene Cutler
> Research Investigator
> Bioinformatics
> Amgen SF
>
>
>
> Mark Reimers,
> senior research fellow,
> National Cancer Inst., and SRA,
> 9000 Rockville Pike, bldg 37, room 5068
> Bethesda MD 20892
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900
http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)
------------------------------
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ArraDx Ltd. Registration Number NI 43067
Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD
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