superpc - 'group' and 'Cox score'
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Liu, Xin ▴ 130
@liu-xin-909
Last seen 10.2 years ago
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 This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk@arradx.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraDx Ltd. Registration Number NI 43067 Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD
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Liu, Xin wrote: > Dear all, > > 1) When we use the package superpc, we run the code got from the tutorial. However, we got the following: superpc is not part of Bioconductor, so you are asking in the wrong listserv. The normal protocol for questions about a contributed R package is to first contact the maintainer (Rob Tibshirani in this case), and if he is unwilling or unable to answer your question, ask on R-help. Jim > "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 > > This e-mail is from ArraDx Ltd > > The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. > > Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. > > If you have received the e-mail in error please notify helpdesk@arradx.com or telephone +44 28 38 363841 and delete the e-mail from your system. > > E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. > > Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. > > ArraDx Ltd. Registration Number NI 43067 > Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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Liu, Xin ▴ 130
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Last seen 10.2 years ago
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----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of bioconductor-request@stat.math.ethz.ch Sent: 23 September 2004 11:02 To: bioconductor@stat.math.ethz.ch Subject: [SPAM] - Bioconductor Digest, Vol 19, Issue 22 - Email found in subject Send Bioconductor mailing list submissions to bioconductor@stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioconductor or, via email, send a message with subject or body 'help' to bioconductor-request@stat.math.ethz.ch You can reach the person managing the list at bioconductor-owner@stat.math.ethz.ch When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioconductor digest..." 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@bbsrc.ac.uk> Subject: [BioC] Metadata for Atgenome1 array To: <bioconductor@stat.math.ethz.ch> Message-ID: <efdaae7f4b83d243868a2f25ad8a4b382c1449@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@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@mail.nih.gov> Subject: [BioC] RE: Advice on print-tip normalization To: bioconductor@stat.math.ethz.ch, "'gcutler@amgen.com'" <gcutler@amgen.com> Message-ID: <16A0583FB1644E4DB8C0A0265028B6FD93044D@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@amgen.com> Subject: [BioC] Advice on print-tip normalization To: bioconductor@stat.math.ethz.ch Message-ID: <8EC0413E-08CF-11D9-95E4-000A95C91324@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@yahoo.com> Subject: [BioC] Regarding Rgraphviz compilation error To: bioconductor@stat.math.ethz.ch Message-ID: <20040922163912.16917.qmail@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@jimmy.harvard.edu> Subject: Re: [BioC] Regarding Rgraphviz compilation error To: Saurin Jani <saurin_jani@yahoo.com> Cc: bioconductor@stat.math.ethz.ch Message-ID: <pine.sol.4.20.0409221253410.27420-100000@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@yahoo.com> Subject: Re: [BioC] Regarding Rgraphviz compilation error To: Jeff Gentry <jgentry@jimmy.harvard.edu> Cc: bioconductor@stat.math.ethz.ch Message-ID: <20040922171116.6335.qmail@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@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@jimmy.harvard.edu> Subject: Re: [BioC] Regarding Rgraphviz compilation error To: Saurin Jani <saurin_jani@yahoo.com> Cc: bioconductor@stat.math.ethz.ch Message-ID: <pine.sol.4.20.0409221316060.27420-100000@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@learnlink.emory.edu> Subject: Re: Fw: [BioC] Affy Bioconductor with Rat230_2 chips To: bioconductor@stat.math.ethz.ch Message-ID: <fc.00249f0f212715f33b9aca007b8705de.2127163b@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@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@picr.man.ac.uk> >To: "Kim Gernert" <gernert@emory.edu> >Cc: <bioconductor@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@stat.math.ethz.ch >> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Kim Gernert >> Sent: 23 April 2004 20:35 >> To: bioconductor@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@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 >person(s) ('the intended recipient') to whom it was addressed. Any views or >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 >constitute a breach of civil or criminal law and is strictly prohibited. If >you are NOT the intended recipient please contact the sender and dispose of >this e-mail as soon as possible. >> >> > > >--- >Outgoing mail is certified Virus Free. >Checked by AVG anti-virus system (http://www.grisoft.com). >Version: 6.0.671 / Virus Database: 433 - Release Date: 4/30/04 > ------------------------------ Message: 8 Date: Wed, 22 Sep 2004 12:02:24 -0700 From: "Bruz Marzolf" <bmarzolf@systemsbiology.org> Subject: Re: [BioC] mas5calls error with YG_S98 CEL files To: <bioconductor@stat.math.ethz.ch> Message-ID: <bfba7186c5b3cb4c8ea0b509fa9090b304eb04@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@systemsbiology.org> > Subject: [BioC] mas5calls error with YG_S98 CEL files > To: <bioconductor@stat.math.ethz.ch> > Message-ID: > > <bfba7186c5b3cb4c8ea0b509fa9090b304eb01@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@yahoo.com> Subject: [BioC] Rgraphviz Error : Rgraphviz.c: In function `Rgraphviz_agopen': To: "'BioConductor mailing list'" <bioconductor@stat.math.ethz.ch> Message-ID: <20040922201714.58656.qmail@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@pnl.gov> Subject: [BioC] Weight functions for Agilent chips (limma) To: bioconductor@stat.math.ethz.ch Message-ID: <af293af0a07c8a44a6098da99d0371309c3dbd@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@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@wehi.edu.au> Subject: Re: [BioC] RE: Advice on print-tip normalization To: "Reimers, Mark (NIH/NCI)" <reimersm@mail.nih.gov> Cc: "'gcutler@amgen.com'" <gcutler@amgen.com>, bioconductor@stat.math.ethz.ch Message-ID: <2254.211.31.120.140.1095892588.squirrel@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@amgen.com> > Subject: [BioC] Advice on print-tip normalization > To: bioconductor@stat.math.ethz.ch > Message-ID: <8EC0413E-08CF-11D9-95E4-000A95C91324@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@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@salk.edu> Subject: [BioC] Problem with gls.series in limma To: bioconductor@stat.math.ethz.ch Message-ID: <2371.10.10.200.247.1095897175.squirrel@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@salk.edu ------------------------------ Message: 13 Date: Wed, 22 Sep 2004 17:02:53 -0700 From: Giovanni Coppola <gcoppola@ucla.edu> Subject: [BioC] limma & targets To: bioconductor@stat.math.ethz.ch Message-ID: <6.1.2.0.2.20040922161857.0415ba00@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@ucla.edu> Subject: Re: [BioC] Weight functions for Agilent chips (limma) To: "Malard, Joel M" <jm.malard@pnl.gov>, bioconductor@stat.math.ethz.ch Message-ID: <6.1.2.0.2.20040922170340.040c1a98@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@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@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@wehi.edu.au> Subject: Re: [BioC] Problem with gls.series in limma To: fhong@salk.edu Cc: bioconductor@stat.math.ethz.ch Message-ID: <6.0.1.1.1.20040923104501.0294cce0@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@salk.edu ------------------------------ Message: 16 Date: Thu, 23 Sep 2004 11:19:18 +1000 From: Gordon Smyth <smyth@wehi.edu.au> Subject: Fwd: Re: [BioC] Problem with gls.series in limma To: fhong@salk.edu Cc: bioconductor@stat.math.ethz.ch Message-ID: <6.0.1.1.1.20040923110558.0295bb70@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@salk.edu >From: Gordon Smyth <smyth@wehi.edu.au> >Subject: Re: [BioC] Problem with gls.series in limma >Cc: bioconductor@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@salk.edu ------------------------------ Message: 17 Date: Thu, 23 Sep 2004 11:46:39 +1000 From: Gordon Smyth <smyth@wehi.edu.au> Subject: Re: [BioC] limma & targets To: Giovanni Coppola <gcoppola@ucla.edu> Cc: bioconductor@stat.math.ethz.ch Message-ID: <6.0.1.1.1.20040923112622.029d4e20@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@cnio.es> Subject: Re: [BioC] RE: Advice on print-tip normalization To: bioconductor@stat.math.ethz.ch Cc: "Reimers, Mark \(NIH/NCI\)" <reimersm@mail.nih.gov>, "'gcutler@amgen.com'" <gcutler@amgen.com> Message-ID: <200409231012.39555.rdiaz@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@amgen.com> > Subject: [BioC] Advice on print-tip normalization > To: bioconductor@stat.math.ethz.ch > Message-ID: <8EC0413E-08CF-11D9-95E4-000A95C91324@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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez 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) ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 19, Issue 22 ******************************************** This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk@arradx.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraDx Ltd. Registration Number NI 43067 Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD
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