Bioconductor Forum

extdata", "agilent_ID.txt", package="human.db0") >myMeta = c("DBSCHEMA"="HUMANCHIP_DB", "ORGANISM"="Homo sapiens", "SPECIES"="Human", "MANUFACTURER"="Agilent", "CHIPNAME"="Human whole genome 8x60k Array ", "MANUFACTURERURL"="http

Annotation probe affy AnnotationDbi Agi4x44PreProcess Annotation probe affy AnnotationDbi

updated 13.5 years ago • Karthik K N

<div class="preformatted">Just wondering if anyone has had any luck creating annotation packages for the HTA 2.0 chip? Best, Stephen On Tue, Sep 10, 2013 at 8:24 PM, Mark Cowley <m.cowley@garvan.org.au> wrote: > Hi Vincent & Benilton, > Myself and Philip de Groot have independently tried to create the > pd.hta.2.0.db overnight with the same error (thou…

BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews

updated 12.1 years ago • Stephen Turner

<div class="preformatted">I'm out of the office until July 28th. Please contact liz higgins if you need assistance @ 636-0163. >>> bioconductor 07/22/06 06:00 >>> Send Bioconductor mailing list submissions to bioconductor at stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/li…

SNP Microarray Annotation GO Network Clustering Survival Cancer hgu133a cdf probe affy

updated 19.5 years ago • Todd Nick

<div class="preformatted">Hi Roy- I don't believe these questions ever got answered, we've been very busy! In the first instance, this looks like a good example of a paired experiment, with matched samples for each patient before and after treatment. I'd suggest filling in the "Tissue" field with the patient ID, so there are two samples with "aaa" and two with "bbb" etc. Then you can set …

GLAD edgeR DiffBind DESeq2 GLAD edgeR DiffBind DESeq2

updated 11.8 years ago • Rory Stark

rep(1:3,each=3) # another true positive >> >> groups <- gl(3,3,labels=letters[1:3]) # organize the data in 3 groups >> >> # basic testing in limma (emprical Bayes) >> require(limma) >> (design1 <- model.matrix

limma limma

updated 16.2 years ago • Gordon Smyth

Environment for R},     author = {{RStudio Team}},     organization = {RStudio, Inc.},     address = {Boston, MA},     year = {2015},     url = {http://www.rstudio.com

R function genomicalignments genomicranges summarizeoverlaps

updated 10.5 years ago • Assa Yeroslaviz

data sets in toto. �So here the > filter condition is (in addition to preliminary filtering by organism > etc., easily done with GEOmetadb) the expression profile.� > > > Now, to get at the expression profile, can I use GEOquery

Cancer GEOquery GEOmetadb Cancer GEOquery GEOmetadb

updated 16.8 years ago • Jack Zhu

RNA-seq/Genome/release102/mouse/index_mouse_r102_gffread_salmon_k31", source = "Ensembl", organism = "Mus musculus", release = "102", genome = "GRChm38", fasta = "/home2/ymwang/linqin/RNA-seq/Genome/release102/mouse/transcript_gffread.fa

DESeq2 fishpond salmon swish

updated 4.3 years ago • Qin

gt;> >>> Hi Shirley, >>> >>> You can find this information in an organism package. ?org.Hs.eg.db for >>> humans (for example). >>> >>> What will be harder will be getting all the information

Organism PROcess biomaRt GenomicFeatures Organism PROcess biomaRt GenomicFeatures

updated 15.4 years ago • shirley zhang

<div class="preformatted">Hi. Sorry for the delay I was not in the office for almost a week (and I left the day before this question popped up). Part of the reason for the confusion here is because the ACCNUM field is supposed to represent the source accessions that were used when designing the package. In that sense ACCNUM is kind of an anachronism since I don't think people really desi…

Annotation GO ChipDb probe

updated 11.3 years ago • Marc Carlson

GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes

updated 11.8 years ago • Vining, Kelly

in 2 (or more) fragments. > > > CEU.RNASeq.geneModel <- easyRNASeq(outputFormat="RNAseq",organism= "HSapiens",count="genes",summarization="geneModels",pattern=".*\\.bam$ ",filesDirectory="../Montgomery2010/bam_hg19/",annotationFile

RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO

updated 13.2 years ago • delhomme@embl.de

include tools which facilitate: * annotation (AnnBuilder, annotate). * data management and organization through the use of the S4 class structure (Biobase, marrayClasses, limma). * identification of differentially

Microarray Annotation Normalization GO Classification Regression Cancer hgu95a cdf probe

updated 22.2 years ago • A.J. Rossini

then you may already have >>>> everything you need. And if you need another organism, you probably >>>> want to look 1st at making an org package using >>>> makeOrgPackageFromNCBI(). And if...gt;>>> some entirely new database resource (IOW you don't want to make an >>>&a…

Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD

updated 12.4 years ago • Sarah Pohl

gt; > Unfortunately there are no readily available packages for annotating > all the new model organism arrays from Affy. However, the functions to > create your own annotation package do exist. If you look at the > AnnotationForge

Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf

updated 12.3 years ago • Joao Sollari Lopes

GenomeStudio to output summarized beadtype values (no bg or > norm), and GenomeStudio always re-organizes the by Sample_Group. I've learned > to double-check that the order in my targets file is the same as the order > coming

Microarray GO limma Microarray GO limma

updated 14.5 years ago • Gordon Smyth

my (rather poor) bioinformatics skills. I have been creating TxDb and BSgenome objects for my Model organism to use your package. My final step would be to create a . db file as the one required in your examples org.Hs.eg.db

CRISPRseek org.hs.eg.db

updated 10.5 years ago • Julie Zhu

not found. >>>> The error was Error in parseKEGGGenome() : Faild to obtain KEGG >> organism >>>> code >>> You need to download the tool set found here >>> (http://www.murdoch-sutherland.com/Rtools

Microarray Cancer AnnBuilder Microarray Cancer AnnBuilder

updated 21.1 years ago • Richard Friedman

<div class="preformatted">And a belated answer to question 3. To match gene ID to GO categories, goseq calls the getgo function with the genome name provided. It then looks up a local variable called .ORG_PACKAGES and will use the organism package that corresponds to the relevant entry in the list. To access this variable type: > goseq:::.ORG_PACKAGES anoGam...the genome…

Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO

updated 13.8 years ago • Matthew Young

Hi, I have analyzed my deep sequencing data with DESeq and successfully generated a heatmap showing differentially expressed miRNAs by using gplots heatmap.2. However, I want to put different colors to the fonts of miRNA names that are shown on y-axis, depending on whether they are up or down regulated. For example, I want to show the names of all down-regulated miRNAs in blue and up-regulated …

SNP Transcription Sequencing RNASeq miRNA Microarray Annotation Normalization GO Cancer

updated 13.9 years ago • Polikepahad, Sumanth

H00882 Cocoon syndrome H01746 STING-associated vasculopathy with onset in infancy ORGANISM Homo sapiens (human) [GN:hsa] GENE 23586 DDX58; DExD/H-box helicase 58 [KO:K12646] [EC:3.6.4.13] 64135 IFIH1; interferon induced

pathview kegg xml

updated 6.4 years ago • anamaria

Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation

updated 13.2 years ago • sun

use one of the org.*.eg.db annotation packages for >> > > this (pick up the one for your organism): >> > > >> > > http://bioconductor.org/packages/release/data/annotation/ >> > > >> > > and use the SYMBOL2EG

Annotation Cancer geneplotter idiogram rtracklayer Annotation Cancer geneplotter idiogram

updated 16.6 years ago • Martin Morgan

<div class="preformatted">Looks like the maintainer made changes but forgot to bump the version (svn revision 77544 and 76958; all svn check-ins should be accompanied by version bumps). Should be fixed when 1.9.2 appears. Martin ----- Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 07/08/2013 09:32 AM, Fr?d?ric Bertrand wrote: > > Hi, > > &…

GO Cancer Rgraphviz clusterProfiler DOSE GO Cancer Rgraphviz clusterProfiler DOSE

updated 12.5 years ago • Martin Morgan

default for circ_seqs in makeTranscriptDbFromBiomart > >>> to be NULL, instead of any organism (human) specific. > >>> > >>> Regards, > >>> > >>> --Malcolm > >>> > >>> > >>> R…

Cancer Organism biomaRt GenomicFeatures Cancer Organism biomaRt GenomicFeatures

updated 13.9 years ago • Malcolm Cook

all of the treatments > (e.g. cancer cells and normal cells from the same subject; different > organs from the same mouse). In this case, the "error" for testing > treatment effects is biological sample * treatment, and the

Microarray GO Preprocessing Cancer vsn Microarray GO Preprocessing Cancer vsn

updated 21.8 years ago • Ramon Diaz

change the default for circ_seqs in makeTranscriptDbFromBiomart to be NULL, instead of any organism (human) specific. Regards, --Malcolm R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale

Cancer Organism biomaRt genomes Cancer Organism biomaRt genomes

updated 13.7 years ago • Malcolm Cook

Chr16" "Chr17" "Chr18" [19] "Chr19" "scaf" And then: print(BSgenome) Black cottonwood genome | | organism: Populus trichocarpa (Black cottonwood) | provider: Phytozome (JGI) | provider version: 3.0 | release date: January 2010

Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer

updated 11.8 years ago • Vining, Kelly

change the default for circ_seqs in makeTranscriptDbFromBiomart > to be NULL, instead of any organism (human) specific. > > Regards, > > --Malcolm > > > R version 2.14.0 (2011-10-31) > Platform: x86_64-apple-darwin9.8.0

Cancer Organism biomaRt GenomicFeatures genomes Cancer Organism biomaRt GenomicFeatures

updated 13.8 years ago • Hervé Pagès

<div class="preformatted">Dear Benilton, thanks for your e-mail. I'm sorry for not having writed back till now, but I have just read it (I don't know why it was not labelled, so I lost it among all the others from bioconductor....) I will try to analyze the arrays I have pending with your script. I will write back soon! Thank you again! Best regards, Elena 2013-11-18 18:44 GMT+01:00 Ben…

BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews

updated 11.7 years ago • Elena Serrano

<div class="preformatted">Hi all, Benilton, could you please update us if there is being some progress in getting the annotation files for HTA 2.0 affymetrix arrays? I am following this topic but I think there's not been any more comment after yours on 11/18/13 and I wonder whether I've missed something about the topic. Thank you in advance! Best regards, Elena Bioinformatician Scientif…

BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews

updated 11.9 years ago • Elena Serrano

<div class="preformatted">Dear Herve, Sean, and All After updating my R, now I can use the liftOver() in rtracklayer package. However I met a problem for SNP rs171. It is on chr 1 in build37.3, but on chr7 in build 36.3. Please check the following link: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=171 In this case, does liftOver work? How many SNPs in NCBI dbSNP like this, map…

SNP GO Cancer SNPlocs rtracklayer SNP GO Cancer SNPlocs rtracklayer

updated 14.2 years ago • shirley zhang

nturaga1 at="" jhmi.edu="">",biocViews = >>>"DNAMethylation",genomebuild = "NCBI Build 36",organism = >>>"Human",species >>>= "Homo Sapiens") >>> makePdInfoPackage(pkg,destDir=".") >> >>==================================================================== ===== >>== &…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.4 years ago • Nitesh Turaga

Chr16" "Chr17" "Chr18" [19] "Chr19" "scaf" And then: print(BSgenome) Black cottonwood genome | | organism: Populus trichocarpa (Black cottonwood) | provider: Phytozome (JGI) | provider version: 3.0 | release date: January 2010

Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer

updated 11.7 years ago • Vining, Kelly

source\_url: http://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/ organism\_biocview: Drosophila\_melanogaster nmask\_per\_seq: 3 SrcDataFiles: AGAPS masks: dm6.agp.gz from http://hgdownload.cse.ucsc.edu

bsgenome drosophila melanogaster bsgnome forge

updated 9.1 years ago • nadia.goue

these basics steps are > explained? which steps are you refrerring to? by the way: which array/organism are you using. and are you doing one or dual color experiments? best T. > Thank you in advance > Massimo > > > > &gt

probe probe

updated 16.2 years ago • Tobias Straub

<div class="preformatted">Hi marc, Thanks for the tip, i realized that my function was too slow. I agree with you. Getting all GO in one shot is a much better approach. On 03/31/2011 09:23 PM, Marc Carlson wrote: > Hi David, > > If this was your function you would 1st of all want to just pass in a > big vector (with your universe of transcript IDs in it) to get …

miRNA Normalization GO Organism GOstats biomaRt microRNA miRNA Normalization GO Organism

updated 14.8 years ago • David

cottonwood) genome as provided by Phytozome (v3, 2013) stored in Bioconductor > Version: 3.0 > organism: Populus trichocarpa > species: Black cottonwood > provider: Phytozome (JGI) > provider_version: 3.0 > release_date

Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO

updated 12.1 years ago • Hervé Pagès

<div class="preformatted">Can you please give us the results of with(ndf, table(MISMATCH, PROBE_CLASS)) the one thing that pdInfoBuilder expects is the PROBE_CLASS field to have the word 'experimental' for thé probes that are not controls. b On 26 Aug 2013 16:44, "Nitesh Turaga" <nturaga1@jhmi.edu> wrote: > Hi Dr.Carvalho, > > Please let me know your thought p…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.3 years ago • Benilton Carvalho

<div class="preformatted">Dear BioC Users, Does anyone have a reference for (or a good definition of) median- interquartile normalization? Is it the same as interquartile normalization? (If not, I would like a reference/definition of both) I have looked for such a definition in the literature, but I haven't found a satisfactory one. Thank you, Monnie McGee Monnie McGee, Ph.D. Associate …

Microarray SystemsBiology Annotation GO Preprocessing Clustering Cancer Yeast Organism GO

updated 18.2 years ago • McGee, Monnie

metabolism in diverse environments" >> [5] "ko00710 Carbon fixation in photosynthetic organisms" >> [6] "ko00562 Inositol phosphate metabolism" >> >> seems to be about what you want, or >> >> >> head(xpathSApply

GO Cancer KEGGSOAP GO Cancer KEGGSOAP

updated 13.8 years ago • Voke AO

<div class="preformatted">Bioconductors: We are pleased to announce Bioconductor 2.11, consisting of 610 software packages and more than 650 up-to-date annotation packages. There are 58 new software packages, and many updates and improvements to existing packages; Bioconductor 2.11 is compatible with R 2.15.1, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. This release inc…

BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage

updated 13.3 years ago • Dan Tenenbaum

lt;- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, >>>> author = "FJ", organism = "Apple", species = "Malus x Domestica cv.GD") >>>> >>>> makePdInfoPackage(arrays, destDir = getwd()) >>>> &gt

Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva

updated 12.5 years ago • Johnson, Franklin Theodore

annotate Imports: methods, AnnotationDbi License: Artistic-2.0 organism: Homo sapiens species: Human manufacturer: Affymetrix chipName: hgu133a2 manufacturerUrl: http://www.affymetrix.com

Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi

updated 14.7 years ago • Martha Behnke

as provided >> by Phytozome (v3, 2013) stored in Bioconductor >> Version: 3.0 >> organism: Populus trichocarpa >> species: Black cottonwood >> provider: Phytozome (JGI) >> provider_version: 3.0 &gt

Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS

updated 12.1 years ago • Hervé Pagès

Here is the previous query with a more descriptive subject. -----Original Message----- From: McGee, Monnie Sent: Thu 10/23/2008 11:14 AM To: bioconductor at stat.math.ethz.ch Subject: RE: Bioconductor Digest, Vol 68, Issue 23 Dear List, Is there an elegant way to obtain the name of a probe set from an Affymetrix platform (doesn't matter which one) corresponding to a given ENTREZ gene ID? It s…

aCGH Sequencing miRNA Microarray Annotation Normalization GO Preprocessing Visualization

updated 17.2 years ago • McGee, Monnie

<div class="preformatted">Bioconductors: We are pleased to announce Bioconductor 2.12, consisting of 671 software packages and more than 675 up-to-date annotation packages. There are 65 new software packages, and many updates and improvements to existing packages; Bioconductor 2.12 is compatible with R 3.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release incl…

BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO

updated 10.5 years ago • Dan Tenenbaum

1:17) is likely not to work with S.pombe. You can see what the > chromosome names are in your organism by inspecting the probeAnno object. > > Best wishes > Wolfgang > > On Sep/8/10 10:33 PM, sohkhan at notes.cc.sunysb.edu

SNP Microarray GO Network Clustering Cancer Organism mgug4122a probe limma convert SNP

updated 15.3 years ago • Daniela Beißer

Sent from my Droid Charge on Verizon 4GLTE "bioconductor- request@r-project.org" wrote: Send Bioconductor mailing list submissions to bioconductor@r-project.org 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@r-project.org You c…

Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy

updated 12.9 years ago • Matthew Thornton

API changes - Support for new schemaless chip packages to allow more flexible suport of non-model organisms in chip packages. - Support for Inparanoid8 objects which contain data from the most recent release of inparanoid

BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage

updated 11.7 years ago • Dan Tenenbaum

I am running Combat on the attached files. 2 channel array (with reference). Problem is the adjusted file returns an added column of numbers where CLID should be. This column then stops delivering said numbers around line 3154, returning to CLID, shifting all the information and data to the left. I am stumped as to why this is happening. Please advise. thanks, tam Reading Sample Information…

Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV

updated 13.2 years ago • SSc Array Core

Bioconductors: We are pleased to announce Bioconductor 2.13, consisting of 749 software packages, 179 experiment data packages, and more than 690 up-to-date annotation packages. There are 84 new software packages, and many updates and improvements to existing packages; Bioconductor 2.13 is compatible with R 3.0.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release in…

BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage

updated 12.2 years ago • Dan Tenenbaum

F,prefix="primeview",fileName="primevie wHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANISM "="Homo sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="Pri meView Human Gene Expression Array","MANUFACTURERURL

Annotation Annotation

updated 12.8 years ago • wang peter