Bioconductor Forum

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

cdf affxparser Harshlight cdf affxparser Harshlight

updated 17.5 years ago • Guido Hooiveld

<div class="preformatted">Why would you need or want to do that? eBayes doesn't destroy any information, so why do you need to avoid it? Gordon > Date: Tue, 31 Aug 2010 19:51:55 +0200 > From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Limma…

affy affy

updated 15.3 years ago • Gordon Smyth

gt; Faculty of Science > IBED/AMB (Aquatische Microbiologie) > Nieuwe Achtergracht 127 > NL-1018WS Amsterdam > the Netherlands > tel. + 31 20 5257089 > fax + 31 20 5257064 </bioconductor></eremenko></div

Normalization limma a4 Normalization limma a4

updated 20.2 years ago • Gordon Smyth

General Hospital 149 13th Street, Room 5408 Charlestown, MA 02129 tshtatland at mgh dot harvard dot edu ############################################################ > library(multtest) > nSam <- 5 > X <- matrix(c(1:nSam, 1:nSam+10), nrow=1) > print(X) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 1 2 3 4 5 11 12 13 …

multtest multtest

updated 17.8 years ago • Timur Shtatland

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld at wur.nl internet: http://nutrigene.4t.com

Microarray probe Microarray probe

updated 13.6 years ago • Gordon Smyth

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

GO GenomicFeatures GO GenomicFeatures

updated 12.4 years ago • Guido Hooiveld

<div class="preformatted">Hi Guido The PPLR method can be used to propagate expression-level uncertainty information into DEG detection. We recommend using the mmgMOS method to identify expression levels and standard errors of these levels, but there is no reason why you couldn't use the standard errors from methods such as fitPLM from the affyPLM package, or MBEI (the "liwong" summary met…

Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe

updated 18.9 years ago • Richard Pearson

of Classification Societies. Invited speakers: D. Banks (USA); P. Hansen (CAN); H. Kiers (NL). - DATA VISUALISATION: D. Cook, Iowa State University (USA). Invited speakers: H. Hofmann (USA); Deborah Swayne (USA); M. Theus (D). - E-STATISTICS

Visualization Bayesian Classification Clustering Regression Visualization Bayesian

updated 22.2 years ago • Wolfgang Huber

of Classification Societies. Invited speakers: D. Banks (USA); P. Hansen (CAN); H. Kiers (NL). - DATA VISUALISATION: D. Cook, Iowa State University (USA). Invited speakers: H. Hofmann (USA); Deborah Swayne (USA); M. Theus (D). - E-STATISTICS

Visualization Bayesian Classification Clustering Regression Visualization Bayesian

updated 21.9 years ago • Wolfgang Huber

TRUE TRUE TRUE TRUE FALSE TRUE TRUE >> libxml fifo cledit iconv NLS profmem cairo >> TRUE TRUE TRUE TRUE TRUE FALSE FALSE >> >> At the compute node: >> =================================================== >>> capabilities() >> …

GO qrqc ASSIGN GO qrqc ASSIGN

updated 13.6 years ago • Sang Chul Choi

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

GO convert GO convert

updated 14.0 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

GO convert minfi bumphunter GO convert minfi bumphunter

updated 10.0 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

updated 13.3 years ago • Guido Hooiveld

<div class="preformatted">Dear Jim, I am facing the same problem, and your idea would be great for me but I ran into a problem: cannot change featureNames of Affybatch. > my.data my.data AffyBatch object size of arrays=744x744 features (23 kb) cdf=HT_HG-U133_Plus_PM (54715 affyids) number of samples=16 number of genes=54715 annotation=hthgu133pluspm notes= > featureNames(my…

GO hgu133plus2 cdf GSVA AnnotationForge GO hgu133plus2 cdf GSVA AnnotationForge

updated 12.5 years ago • steven wink

libraries: readline, BLAS(generic) Additional capabilities: PNG, JPEG, iconv, MBCS, NLS Options enabled: R profiling Recommended packages: yes 2) then I install R and bioconductor as % make instll in R: > source

cdf cdf

updated 20.4 years ago • xnyang@seu.edu.cn

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

Annotation GO Annotation GO

updated 13.8 years ago • Guido Hooiveld

Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld at wur.nl > internet

Annotation GO Organism OrgDb Annotation GO Organism OrgDb

updated 13.8 years ago • Marc Carlson

lt;- as.character(substitute(package)) if (package %in% c("ctest", "eda", "modreg", "mva", "nls", "stepfun", "ts")) { have.stats <- "package:stats" %in% search() if (!have.stats) require("stats") warning("package ", sQuote(package), " has been

GO geneplotter graph Rgraphviz pamr globaltest GO geneplotter graph Rgraphviz pamr

updated 21.1 years ago • David Rocke

gt;>>>>> Wageningen University Biotechnion, Bomenweg 2 >>>>>>> NL-6703 HD Wageningen >>>>>>> the Netherlands >>>>>>> tel: (+)31 317 485788 >>>>>>> fax: (+)31 317 483342

Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma

updated 16.5 years ago • James W. MacDonald

xsv8vT5PZ T655z/ AGNl/l6AsFKr/wAnsp9c85/sbL/L0+T2U+uec/2Nl/l6AsFKr/yeyn1zzn+xsv8AL0+T2U +uec/2 Nl/l6AsFKr/yeyn1zzn+xsv8vT5PZT655z/Y2X+XoCwUqv8Ayeyn1zzn+xsv8vT5PZT655 z/AGNl /l6AsFKr/wAnsp9c85/sbL/L0+T2U+uec/2Nl/l6AsFKr...xsv8AL0+T2U+uec /2Nl/l 6AsFKr/yeyn1zzn+xsv8vT5PZT655z/Y2X+XoCwUqv8Ayeyn1zzn+xsv8vT5PZT655z/AG Nl/l6A sFKr/TEt77TnrK9yM9/7DkFhhmnSNX4G2gk0fDRVPmkb3VYKAVn+IwnWGL6v6jz/AMXYOX 459m/E…

updated 23.1 years ago • Sundaram, Shyam NIH/CIT

This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1903392753-1517917941-1027454075=:15954 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII When I select the "Files" button on the 'MarrayRaw builder' window, the 'File Browser' window sh…

updated 23.4 years ago • Dick Beyer