Bioconductor Forum

keytype="ENTREZID", column="SYMBOL") head(y$genes) But I'm working on a not-so-common organism, for which no default packages are available.Then, I skipped this step, and I was able to perform a statistical analysis

annotation entrez gene ids software error

updated 6.7 years ago • Raito92

Hi All I'm new to using this particular package but i have great hopes for it. I work on a model organism which is not currently supported. I have build a package using the following code: makeOrgPackageFromNCBI(version

R software error annotationforge

updated 7.7 years ago • laural710

ndf, xysFile = xys,posFile = pos, author = "AR", biocViews = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens") > makePdInfoPackage(seed, destDir = "./") ====================================================================== ====== ==== Building annotation package for Nimblegen Tiling

Annotation Organism oligo pdInfoBuilder Annotation Organism oligo pdInfoBuilder

updated 15.9 years ago • Alex Rodriguez

beniltoncarvalho@gmail.com", biocViews="AnnotationData", genomebuild="hg19", organism="Homo sapiens", species="Homo sapien", url="http://about.me/benilton") makePdInfoPackage(seed, destDir=".") ## end If you have any

Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder

updated 11.9 years ago • Benilton Carvalho

count.table <- easyRNASeq(system.file( "extdata", package="RnaSeqTutorial"), organism="Dmelanogaster", readLength=36L, annotationMethod="gff", annotationFile=system.file( "extdata", "annot.gff", package

Annotation BSgenome BSgenome IRanges easyRNASeq Annotation BSgenome BSgenome IRanges

updated 13.0 years ago • Vince Schulz

glutamicum_ ATCC13032 (Bielefeld) KEGG pathway, but unfortunatly this is not working wiht my organism. I found an example for _B. subtilis _which is working pretty fine, but changing the species name ( i looked it up in the

pathview Kegg rnaseq data visualization

updated 9.5 years ago • rafre

mySrcUrls, baseMapType = myBaseType, otherSrc = myOtherSrc, pkgName = "testPkg", pkgPath = myDir, organism = "human", version = "1.1.0", makeXML = TRUE, author = list(author = "kees", maintainer = "kees@myemail.com"), fromWeb = TRUE) [1] "It may take...srcUrls=mySrcUrls, >>> baseMapType=myBaseType, >> pkgName="myPkg", pkgPath="C:\tmp", organism="human", makeXML…

Annotation GO Cancer Organism Biobase annotate AnnBuilder PROcess bridge Annotation GO

updated 21.3 years ago • Floor Stam

Hi- I'm trying to analyze some Sorghum NGS transcriptome data using topGO. The analysis runs using my custom geneID2GO object and the annFUN.gene2GO function. When I run GenTable, however, the results are strange. For example, for the GO:0006970 category, the geneID2GO mappings I used only lists 48 genes annotated to this category, but the GenTable function claims that 335 genes are annotated a…

GO Category topGO GO Category topGO

updated 12.3 years ago • Diana Toups Dugas

I am creating my annotation package using makeOrgPackage(). I followed the instruction here: http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation Forge/inst/doc/MakingNewOrganismPackages.htm This are the dataframes and the commands I used: > test3 GID Gene Name Protein Name 1 PSE\_0724 PSE\_0724 GCN5-related N-acetyltransferase 2 PSE\_0725 PSE\_0725 GCN5-related N-acetyl…

annotationforge Annotation GO

updated 11.3 years ago • artur

Hi Diana, the 'issue' you are seeing is due to the "True Path Rule". I suspect that the geneID2GO mappings gives only the specific annotation to a particular GO term. However during the mapping of the genes to the GO hierarchy the genes annotated to a GO term are pushed up the hierarchy. So a GO term will contain the genes specifically annotated to it plus all the genes present in the children …

Annotation GO topGO Annotation GO topGO

updated 12.3 years ago • Adrian Alexa

the rhdf5 package (version 2.38.1) The file is organized as shown in this image: ![H5 file organization][1] Here's my problem: When I try to 1)load the full TPC_tables group in a variable or 2) read TPC tables which are quite

H5DRead MemoryError

updated 3.0 years ago • julien.ballbe

I am rerunning some bulk samples thru my pipeline, but am including more samples from various organs of individuals from either sex and also considering symbiotic state. My ```All.coldata``` looks like this: ``` > All.coldata

DESeq2

updated 2.3 years ago • john.briseno

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

biomaRt biomaRt

updated 13.9 years ago • Malcolm Cook

using this function. Here's my call the easyRNASeq function: dgeList <- easyRNASeq(organism="Hsapiens", annotationMethod="biomaRt", gapped=TRUE, count="exons", filesDirectory = "/media/sf_Storage1/RNAseq", pattern

BSgenome BSgenome edgeR easyRNASeq BSgenome BSgenome edgeR easyRNASeq

updated 13.1 years ago • Guest User

with the ReactomePA, but I get the following result: <pre> > y <- gsePathway(geneList_entrez, organism="mouse", nPerm = 100, minGSSize = 20,pvalueCutoff = 1, pAdjustMethod = "BH", exponent=1, verbose = T) [1] "calculating observed enrichment

ReactomePA gsePathway

updated 10.8 years ago • samuel collombet

s because of the way that the database was built. The data in pathway to gene is limited to those organisms that we produce annotation packages for here. Marc On 10/12/2011 02:39 PM, Peng Yu wrote: > Hi, > > There are 292 pathways

Pathways Pathways

updated 14.2 years ago • Marc Carlson

library(AnnotationDbi) Illumina_8v <- 'ilmn_cust_raw.txt' myMeta = c("DBSCHEMA"="illumina", "ORGANISM"="Homo sapiens", "SPECIES"="Human", "MANUFACTURER"="Illumina", "CHIPNAME"="Illumina pre-release", "MANUFACTURERURL"="http://www.illumina.com

Annotation affy AnnotationDbi Annotation affy AnnotationDbi

updated 15.9 years ago • John Lande

subset.gff") > txdb <- makeTxDbFromGFF(file=gff.file.small, format="auto", dataSource=url, organism="Vitis vinifera", taxonomyId=29760, chrominfo=data.frame(chrom="ctg123", length=1497228, is_circular=FALSE)) Import

maketxdbfromgff genomicfeatures

updated 9.7 years ago • TimothéeFlutre

and haplotype construction * Manage data (acquisition, validation, quality control, organization) * Analyze data, interpret and present results * Adapt or develop new statistical tools when necessary * Optimize

Microarray Genetics Normalization Clustering Microarray Genetics Normalization Clustering

updated 22.2 years ago • Sophie Gallina

gene.idtype="entrez",i.e. Entrez Gene, which are the primary KEGG gene ID for many common model organisms. For other species, gene.idtype should be set to "KEGG" as KEGG use other types of gene IDs. For more details check the...also works. I have one question, why do you not accept the native IDs that KEGG uses for some organisms. My specific example is for Arabidopsis. KEGG uses TAIR ids, a…

Network convert pathview Network convert pathview

updated 11.7 years ago • Luo Weijun

Okay, I've been banging my head against this wall for too long, and it can't just be me having this problem. I'm not even sure this is the appropriate place to ask — if it's not, can someone point me to the correct forum? I'd like to be able to use PhyloSeq's \`tip\_glom()\` or something similar to group closely related organisms in metabarcoding studies (16S amplicons), and have annotations wit…

ggtree treeio phyloseq annotation tip_glom

updated 7.9 years ago • werdnus

gapped=F, validity.check=TRUE, chr.map=chr.map, organism="custom", annotationMethod="env", annotationObject=exon.range, count="genes", filenames=files, summarization="geneModels...F, + …

Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq

updated 12.3 years ago • Guest User

0.1-10" "1.10.0" "0.99-7" "1.10.0" > > >mySrcUrls <- getSrcUrl("all", organism="Mus Musclusus") > >base<- file.path(.path.package("AnnBuilder"), "data", "lgtc.ids.1.txt") > >myBaseType<- "gbNRef...gt; pkgName = "lgtc201106", > pkgPath = ".", > …

Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn

updated 19.1 years ago • John Zhang

Nov-01 # | 1 position frequency matrices from 1 source: # | JASPAR_CORE: 1 # | 1 organism/s # | Hsapiens: 1 # Hsapiens-JASPAR_CORE-FOXA1-MA0148.1 # now use rGADEM to do a seeded search: pwm.foxa1 <- as.list(MotifDb

rGADEM MotifDb rGADEM MotifDb

updated 12.8 years ago • Paul Shannon

currently supported by multiple types of funding, such as NIH and other federal grants, non-profit organization grants, funds from industry, and funds from philanthropic donors. A successful candidate will * work with interdisciplinary

Bioinformatician/biostatistician position Job

updated 9.2 years ago • lfrank8

vicPac2" I just thought it was odd for the package not to work out of the box for the model organism C. elegans. It also wouldn't work for pig, and maybe more. Thank you! [[alternative HTML version deleted]] </div

GO Yeast Organism goseq genomes GO Yeast Organism goseq genomes

updated 11.7 years ago • François Lefebvre

issue? This is not something you need to > do. The GO and KEGG packages are separate from the organism > packages. You might want to look at the vignette in annotate for an > overview. I used the "datasets manager" pull

GO Cancer annotate GO Cancer annotate

updated 21.6 years ago • Richard Friedman

<div class="preformatted"> >[BioC] limma's eBayes error: No residual degrees of freedom in linear model >Li,Qinghong,ST.LOUIS,Molecular Biology Qinghong.Li at rdmo.nestle.com >Tue Nov 15 22:09:13 CET 2005 > >Hi BioC, > >I was runing eBayes and got the above error. I searched the old archives >of BioC, and has found similar problem pose…

limma limma

updated 20.1 years ago • Gordon Smyth

follows I have an error. thanks, Francesco > countDataSet <- easyRNASeq(filesDirectory=getwd(), + organism="HSapiens", + chr.sizes=as.list(seqlengths(Hsapiens)), + readLength=100L, + annotationMethod="biomaRt", + format="bam", + …

RNASeq Alignment BSgenome BSgenome RNASeq Alignment BSgenome BSgenome

updated 13.9 years ago • Lescai, Francesco

limma kegga goanna

updated 10.0 years ago • Guido Hooiveld

consider using bioperl if you have access to it. Better yet, if these are sequences from the same organism, just use blat and the output is tab-delimited text which you can load directly into R. If you use blat, you can just do

probe probe

updated 20.9 years ago • Rohit Ghai

Note that we provide a few "TxDb" packages that contain pre-computed TranscriptDb objects for a few organisms and tracks: http://bioconductor.org/packages/release/BiocViews.html#___Transcri ptDb There is one for hg19/knownGene...warning is working properly, you can get a legitimate warning like this for some combination of UCSC organism/track (but AFAIK never for the knownGene track). If all…

Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb

updated 11.6 years ago • Hervé Pagès

lt;- as.character(DF\_with\_EntrezID\_subsetentrezgene) >res=spia(de=sig\_genes, all=all\_genes, organism="hsa",plots=TRUE) __Error in spia(de = DE, all = all\_genes, organism = "hsa", plots = TRUE) :    de must be a vector of log2 fold

SPIA named vectors pathway analysis

updated 11.2 years ago • A Eelmur

wanting to analyze my ATACseq dataset, and have been struggling a bit. I am working with a non-model organism and am trying to work through some ATACseqQC tutorials, specifically this one regarding footprint plotting: https

ATACseqQC

updated 22 months ago • Konrad

an R01 from the NCI’s [Center to Reduce Cancer Health Disparities](https://www.cancer.gov/about-nci/organization/crchd). Interested candidates should send a cover letter and CV/resume to Dr. Joshua Campbell (camp@bu.edu). **Advantages

DNASeq RNASeq SingleCell

updated 4.4 years ago • camp

<div class="preformatted"> Dear Bioconductor team, I am currently using the oligo package for analyzing tiling array data (Affymetrix GeneChip Human Tiling 2.0R Array). I made a PlatformDesign package (pd.hs35b.p02r.v01_0.0.1) using the makePdInfoPackage function from pdInfoBuilder package. The .bpmap file used to make this package was downloaded from the Affymetrix website at http://www.a…

BiocViews Organism biocViews oligo pdInfoBuilder BiocViews BiocViews Organism biocViews

updated 13.8 years ago • Guest User

hgKEGG <- hyperGTest(params) summary(hgKEGG) # Error in get(paste(annotation(object), "ORGANISM", sep = "")) : # variable "org.Hs.eg.dbORGANISM" was not found hgKEGG at annotation <- "org.Hs.eg" summary(hgKEGG) # KEGGID Pvalue

Microarray Annotation Escherichia coli hgu95av2 Microarray Annotation Escherichia coli

updated 17.1 years ago • James F. Reid

nbsp;  txdb <- makeTxDbFromGFF("/path/to/gencode.v19.annotation.gtf", dataSource="Gencode", organism="Homo sapiens", format="gtf") Now I get the following output:      Import genomic features from the file

software error R bioconductor genomicfeatures error message

updated 8.8 years ago • Walter F. Baumann

sampleTable) <- colnames(txi$counts) dds <- DESeqDataSetFromTximport(txi, sampleTable, ~ organ) ######Here I have 2 possibilities : ###First (basic DESeq2 usage) : dds <- DESeq(dds) normalised_count <- counts(dds, normalized

deseq2 salmon tximport normalization

updated 6.8 years ago • Alex So

used to generate my read count table below: read.count <-easyRNASeq(format='bam',readLength=50L, organism="Mmusculus", chr.sizes="auto", annotationMethod="gtf", annotationFile="mm9.ensgene.gtf", count="genes", summarization

RNASeq Annotation PROcess DESeq RNASeq Annotation PROcess DESeq

updated 13.2 years ago • Guest User

lt;- easyRNASeq(filesDirectory=getwd(), filenames="accepted_hits.sorted.bam", organism="Hsapiens", chr.sizes="auto", annotationMethod="gtf", annotationFile="/x400ifs-accel/ntteam/hufuyan/humanindex/Ensembl

Annotation easyRNASeq Annotation easyRNASeq

updated 12.8 years ago • Guest User

I'm trying to design a CRISPR gRNA and search for off-targets with CRISPRseek. My organism has a very rough draft genome that is organized into ~160,000 scaffolds. I've been able to forge a BSgenome package...I'm trying to design a CRISPR gRNA and search for off-targets with CRISPRseek. My organism has a very rough draft genome that is organized into ~160,000 scaffolds. I've been able to forge …

crisprseek grna searching bsgenome forge offtarget analysis

updated 9.6 years ago • rajewski23

NA 10012_spt 538 10013_spt 2050 10014_spt 1360 my URLs are: x<-getSrcUrl("all", organism="Homo sapiens") my QC output is: E5annEGQC [1] "\n\nQuality control information for E5annEG \nDate built: Created: Fri Aug

Annotation GO probe annotate AnnBuilder Annotation GO probe annotate AnnBuilder

updated 19.4 years ago • Dario Greco

div class="preformatted">Dear Bioconductor users, I'm working on a novel organism (no genome, only a reference transcriptome I had prepared with Trinity) and I have to do some differential gene expression

Sequencing GO Organism edgeR DESeq EBSeq Sequencing GO Organism edgeR DESeq EBSeq

updated 11.6 years ago • Nicole Ertl

Db type: TxDb \# Supporting package: GenomicFeatures \# Data source: EctsiV2\_all.gtf \# Organism: NA \# miRBase build ID: NA \# Genome: NA \# transcript\_nrow: 18406 \# exon\_nrow: 162850 \# cds\_nrow: 136291 \# Db created by: GenomicFeatures...Db type: TxDb \# Supporting package: GenomicFeatures \# Data source: EctsiV2\_all.gtf.gff3 \# Organism: NA \# miRB…

gtf TxDb maketxdbfromgff

updated 10.5 years ago • yacine.badis

<div class="preformatted">Greetings to all and apologies for any cross-postings. If you know of anyone else who could benefit from this announcement please forward to them. Best regards and good luck to everyone, Michael O'Connell. BioConductor Project and Insightful Corp. Collaboration Announcement This week, Insightful Corporation announced the availability of S+ArrayAnalyzer version 2.0,…

Microarray SAGE Annotation Infrastructure Microarray SAGE Annotation Infrastructure

updated 21.6 years ago • MOConnell@insightful.com

Hi all, I'm trying to create an organism package (I've did it in the past with no problems), but now I'm experiecing a weird error. I've used the example in the vignette...copy and paste the code form the vignette: library("AnnotationForge") ## Makes an organism package for Zebra Finch data.frames: finchFile <- system.file("extdata","finch_info.txt",package="Annot…

makeOrgPackage

updated 4.9 years ago • Eduardo Andres-Leon

Linux command line experience - High level of motivation, creativity, self-responsibility and self-organization **Our offerings:** - Challenging and varied tasks with a high degree of personal responsibility - Support from and

Epigenomics NGS Aging Biobase

updated 18 months ago • arne.sahm

Can anyone help me understand why requireNamespace("org.Hs.eg.db") not only loads the needed name spaces, but also loads DBI and RSQLite into the search space? It isn't usual practice in R that loading a name space will have a side-effect like this. For example requireNamespace("AnnotationDbi") doesn't add anything to the search path, even though AnnotationDbi uses both DBI and RSQLite. Is loadi…

org.hs.eg.db DBI rsqlite

updated 9.7 years ago • Gordon Smyth

baseName = myBase, baseMapType = myBaseType, pkgName = "hs95av2Entrezg7", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "Weijun", maintainer = "Weijun <luo_weijun at="" yahoo.com="">"), fromWeb =T) print

Microarray Annotation probe annotate affy AnnBuilder Microarray Annotation probe annotate

updated 19.5 years ago • Luo Weijun

email = "email", biocViews = "AnnotationData", genomebuild = "unspecified", organism = "unspecified", species = "unspecified") makePdInfoPackage(seed, destDir = ".")</pre> This is the error: <pre> ================================================================================ Building annotation

microarray R oligo micro array data annotation

updated 10.4 years ago • zenekzkk

<div class="preformatted">Dear list members, short version of my question: How can I determine, whether it improves the model quality of a linear model (in limma), when I introduce additional explanatory variables? Is there an equivalent to feature selection (as in machine learning) for choosing the explanatory variables? The complete story: We analyse a dataset of about ninety single cha…

Microarray limma Microarray limma

updated 16.3 years ago • Andre J. Aberer

computational model of biological systems, from the molecular level to larger pathways, cellular and organism-level systems. GO defines an ontology is composed of classes (or concepts) that can be used to describe gene function

gene ontology go ontology bioinformatics genomics News

updated 7.3 years ago • laurent.albou

Beijing Genomics Institute (BGI), Shenzhen, China We look forward to seeing you in Boston! The organizers and chairs of CAMDA 2014 Chairs: Djork-Arn? Clevert, Johannes Kepler University, Austria Joaquin Dopazo, CIPF, Spain

Genetics Cancer Genetics Cancer

updated 11.8 years ago • Djork Clevert

panfs/storage.local/genacc/home/sr09m/Biomedicine research/New Drosophila analysis/Tophat_temp", organism = "Dmelanogaster", chr.sizes = as.list( seqlengths( Dmelanogaster )), readLength = 76L, annotationMethod = "gff", annotationFile

Organism edgeR easyRNASeq Organism edgeR easyRNASeq

updated 13.4 years ago • delhomme@embl.de

samples. > 2. I have 12 different samples which were collected from 3 different positions of an organ from 2 > species at 2 stages (3*2*2=12 samples). I did RNA-seq and sequenced them in 12 lanes, > respectively. I want to see the

Normalization Clustering edgeR Normalization Clustering edgeR

updated 15.5 years ago • Gordon Smyth

single channel DNA microarray dataset where normal and diseased tissue are taken from the same organ from 5 persons. So I have 10 CEL files with me. Now I want to analyse the differential gene expression between the normal

limma design matrix limma paired analysis limma

updated 8.3 years ago • anandprem1792

channel microarray experiment. - The data was produced using the ScanArray Express scanner. - The organism of interest is Campylobacter jejuni; it is exposed to two conditions (treatment and control). - I've managed to derive

Organism probe convert GOstats Organism probe convert GOstats

updated 11.9 years ago • Guest User

number of complex datasets inform our biological understanding of both the normal workings of organisms in biology and processes which cause disease. The analysis of these datasets, which has become an increasingly

updated 18.2 years ago • Wolfgang Huber

Hello, I am trying to quantify human transcripts mapped with salmon in some RNA sequencing (GSE107467) using tximeta. This is the code I use to import the annotation file and the transcript file. dir2 <- system.file("extdata", package="tximeta") indexDir <- file.path(dir2, "gencode_v29_idx") fastaFTP <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencod…

rnaseq tximeta

updated 6.1 years ago • MT