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 email: guido.hooiveld@wur.nl<mailto:guido.hooiveld

Proteomics GO PROcess Proteomics GO PROcess

updated 14.9 years ago • Guido Hooiveld

11 PM, Stephanie M. Gogarten >>> <sdmorris@u.washington.edu <mailto:sdmorris@u.washington.**edu<sdmorris@u.washington.edu="">>> >>> wrote: >>> >>> It's not finding any BAF values that meet all the criteria...Stephanie M. Gogarten >>> <sdmorris@u.washing…

SNP Annotation cdf GWASTools SNP Annotation cdf GWASTools

updated 12.5 years ago • Sam Rose

lt;- as.matrix(a[,2:11]) rownames(counts) <- a$gene_id design=cbind(NH=c(1,1,1,1,1,0,0,0,0,0),NL=c(0,0,0,0,0,1,1,1,1,1)) v <- voom (counts, design, plot=TRUE)</pre> <span style="line-height:1.6">Could you please help me in solving my problem

voom TCGA RNAseq

updated 11.1 years ago • paola.ostano

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

updated 16.5 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 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

Normalization vsn limma Normalization vsn limma

updated 15.9 years ago • Guido Hooiveld

Regards, James > y <- rnorm(20) > x <- 1:20 > library(nlme) Loading required package: nls > out <- gls(y~x) > summary(out) Generalized least squares fit by REML Model: y ~ x Data: NULL AIC BIC logLik 63.18472 65.85584

Microarray Genetics Microarray Genetics

updated 23.0 years ago • James Wettenhall

student Erasmus MC Department of Pathology JNI,Room H Be-302 Dr. Molewaterplein 50 3015 GE Rotterdam-NL phone: +3110-7043093 fax: +3110-7044762 r.kandimalla at erasmusmc.nl http://www.erasmusmc.nl/pathologie </div

limma limma

updated 17.2 years ago • r.kandimalla

analysis, but I have found nothing. I understand that it is probably possible to fit such data using nls, or mixtools packages. But I wonder if there is any easiest way to do so? My own problem with e.g. Dean-Jett-Fox model than I don

Clustering flowStats Clustering flowStats

updated 13.1 years ago • Guest User

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

Biostrings biomaRt Biostrings biomaRt

updated 17.2 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 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

miRNA Annotation db0 AnnotationDbi miRNA Annotation db0 AnnotationDbi

updated 16.2 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 13.2 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 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

Transcription Annotation BSgenome annotate Biostrings BSgenome Transcription Annotation

updated 17.2 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

sva sva

updated 13.1 years ago • Guido Hooiveld

<div class="preformatted">> Date: Thu, 17 Nov 2005 22:10:33 +0100 > From: Nataliya Yeremenko <eremenko at="" science.uva.nl=""> > Subject: [BioC] About weight function for Agilent data > To: Bioconductor List <bioconductor at="" stat.math.ethz.ch=""> > > I have seen here in the BioC topics several threads concerning weighting of >…

Normalization Normalization

updated 20.1 years ago • Gordon Smyth

to Apply__ If you are interested please contact Rachel Myers [rachel(dot)myers(at)duke(dot)edu](mailto:rachel.myers@duke.edu), with subject line CAGPM BioStat III.  Additionally, please apply to the&nbsp

rnaseq precision medicine biomarker genomics Job

updated 7.8 years ago • ram330

<div class="preformatted">Hi everyone We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run. It goes fine until section 5, were it is interrupted by an error > arrayQualityMetrics(rawAffyData, outdir="quality", force=T) The report will be written into directory 'quality'. [[1]] [[2]] [[3]] [[4]] Er…

arrayQualityMetrics arrayQualityMetrics

updated 14.9 years ago • Paulo Nuin

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

limma GLAD limma GLAD

updated 20.1 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

limma limma

updated 12.5 years ago • Guido Hooiveld

gt;Faculty of Science >IBED/AMB (Aquatische Microbiologie) >Nieuwe Achtergracht 127 >NL-1018WS Amsterdam >the Netherlands </div

limma arrayMagic limma arrayMagic

updated 20.2 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

Microarray Annotation ChipName Microarray Annotation ChipName

updated 12.3 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 12.1 years ago • Guido Hooiveld

the Annual Meeting will be covered by CS. Contact for information and nominations: prinssc (at) jmu (.) edu CS: http://www.classification-society.org/csna [[alternative HTML version deleted]] </div

Classification Classification

updated 17.4 years ago • William Shannon

<div class="preformatted">Dear Guido, Since Bioconductor has compiled the Windows version of xps using root 5.22.00 you need to install the binary of this version, as mentioned in "System Requirements". You can download this version from: http://root.cern.ch/root/Version522.html I would suggest to install version: root_v5.22.00.win32.vc90.msi Please see also my introductory comments for W…

Annotation GO xps Annotation GO xps

updated 16.4 years ago • cstrato

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

Normalization vsn limma convert Normalization vsn limma convert

updated 16.1 years ago • Guido Hooiveld

process, please contact the Principal Investigator directly: yuzun at pennstatehealth psu edu. This is a limited-term non-tenure line position funded for one year from date of hire, with possibility of refunding. Employment

postdoc Computational Bioinformatics Biology Genomics

updated 2.7 years ago • yuzun

FALSE ? ?FALSE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE ? ? TRUE ?libxml ? ? fifo ? cledit ? ?iconv ? ? ?NLS ?profmem ? ?cairo ? ?TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ?FALSE > library(tcltk) Loading Tcl/Tk interface ... Error : .onLoad failed in loadNamespace

updated 15.6 years ago • Sonia Leach

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

Normalization vsn limma Normalization vsn limma

updated 16.3 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 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

moe430a multtest affy limma moe430a multtest affy limma

updated 16.5 years ago • Guido Hooiveld

<div class="preformatted">Dear Agnieszka, My guess is that you need to background correct using backgroundCorrect() before using mergeScansRG(). If problems persist, I suggest you write directly to the function author. See help("mergeScansRG") for that info. Best wishes Gordon > Date: Thu, 26 Jan 2012 10:34:33 +0100 > From: Agnieszka ?mie?ko <akisiel at="" ibch.poznan.p…

Microarray limma Microarray limma

updated 13.9 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 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

Annotation moe430a Annotation moe430a

updated 16.5 years ago • Guido Hooiveld

2. What is the "difference of differences" between phenotype1 (TRUE vs FALSE) and SampleType (L vs NL)? 3. What are the DEGs between Lesional and Non-Lesional samples, for those with Phenotype1=<false> **regardless** of phenotype

limma

updated 2.7 years ago • Jonathan

Hi there! I have been looking at foldGO today, and wanted to try its functions on some of my own data, following the workflow published on Bioconductor (https://www.bioconductor.org/packages/release/bioc/vignettes/FoldGO/inst/doc/vignette.html). However, I quickly ran into an error, although I believe all my inputs have the right format. I have a dataframe containing Gene.IDs and fold c…

FoldGO GSEA

updated 5.1 years ago • lessismore

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

Annotation GO xps Annotation GO xps

updated 16.4 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

convert convert

updated 12.8 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

Microarray Microarray

updated 11.8 years ago • Guido Hooiveld

<div class="preformatted">Hi Guido, you could create a file containing the microRNA ID and it's corresponding Gene ID (NCBI) and then use SQLForge to create a custom annotation package which would use an organism .db0 package. HTH, J. Hooiveld, Guido wrote: > Dear list, > > Question for the more knowledgable people: > A collegue and I would like to create an a…

miRNA Annotation Organism db0 AnnotationDbi microRNA miRNA Annotation Organism db0

updated 16.2 years ago • James F. Reid

1.0.2 mgu74av2cdf 1.4.3 mgu74av2probe 1.0 # R 1.8.1patched package versions base 1.8.1 ts 1.8.1 nls 1.8.1 modreg 1.8.1 mva 1.8.1 ctest 1.8.1 methods 1.8.1 affy 1.3.28 eda 1.8.1 Biobase 1.4.0 reposTools 1.3.6 MASS 7.1

cdf gcrma cdf gcrma

updated 21.7 years ago • Dick Beyer

Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > > internet: http://nutrigene.4t.com > email: guido.hooiveld at wur.nl > > &gt

probe probe

updated 18.6 years ago • Henrik Bengtsson

<div class="preformatted">Hi Anand, Many thanks for your interest in our work on spatial artefacts. Our current belief is to do things in the following order 1) Detect the phenomena described in the Smith et al (2010) paper. You do need to run generateNeighbours before many of these functions. The number of beads detected at this stage should be relatively small, and would probably be rem…

Cancer beadarray EBImage Cancer beadarray EBImage

updated 15.1 years ago • Mark Dunning

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

Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder

updated 15.7 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

Annotation Annotation

updated 13.2 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

updated 13.2 years ago • Wolfgang Huber

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

hgu133a hgu133a

updated 14.5 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 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

probe gcrma probe gcrma

updated 17.0 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

miRNA cdf affy miRNA cdf affy

updated 12.0 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

cdf affy convert cdf affy convert

updated 13.6 years ago • Guido Hooiveld

For the following code vignette, **Src** is the sample origin in which **CN** is controls, **NL** is non-lesional, **LS** is lesional; **Pheno** ("Y"/"N") is whether cohort samples have the phenotype or not; I use **"B"** for phenotype-agonistic

limma

updated 2.3 years ago • Jonathan

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 14.0 years ago • Guido Hooiveld

gt;Maintainer: Gordon Smyth <smyth@wehi.edu.au> >Depends: methods, modreg, MASS, splines, nls, nlme, R (>= 1.6.1) >Description: Data analysis, linear models and differential expression for >spotted and oligonucleotide

Microarray Normalization limma Microarray Normalization limma

updated 22.5 years ago • Gordon Smyth

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

Normalization Biobase vsn limma marray Normalization Biobase vsn limma marray

updated 19.7 years ago • Nataliya Yeremenko

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

limma limma

updated 12.1 years ago • Gordon Smyth

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

Normalization Biobase vsn limma marray convert Normalization Biobase vsn limma marray

updated 19.7 years ago • Nataliya Yeremenko

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

Normalization limma a4 Normalization limma a4

updated 20.2 years ago • Nataliya Yeremenko

<div class="preformatted">hi i get an error when trying to install R 2.9.1 from source on an intel mac os 10.5.7. i have used the gcc4.2 from xcode 3.1 and gfortran 4.2 from http://r.research.att.com/tools/. i also tried using gcc and gfortran 4.3 installed with macports. same error. im not an expert in this and im a bit lost as to the "source" of my problem? here follows some of the out…

updated 16.4 years ago • Jesper Ryge

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

affy affy

updated 15.3 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

Microarray Normalization GO limma Microarray Normalization GO limma

updated 11.8 years ago • Gordon Smyth

General Hospital 149 13th Street, Room 5408 Charlestown, MA 02129 tshtatland at mgh dot harvard dot edu ############################################################ ## read *only* the gcrma-processed dataset (nothing else) into a new R session ## to reduce the number of objects in memory: > load

genefilter PROcess genefilter PROcess

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 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

cdf affy affxparser cdf affy affxparser

updated 15.9 years ago • Guido Hooiveld

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

convert convert

updated 12.8 years ago • Guido Hooiveld

General Hospital 149 13th Street, Room 5408 Charlestown, MA 02129 tshtatland at mgh dot harvard dot edu ############################################################ > B <- 1000 > seed <- 99 > TTBoot <- MTP(X=esetGcrmaExprsFiltered, Y=TT, test = "t.twosamp.unequalvar", alternative = "two.sided

multtest multtest

updated 17.8 years ago • Timur Shtatland