Bioconductor Forum

  Hi all, There have been a number of questions asked on this topic (I've linked the relevant threads below), but I'm not sure if anyone has found a working solution.  I have run GOSeq on my gene set and am looking to __identify the genes in each category (numDEInCat)__.  Here is what I've done so far. &nbsp...relevant threads below), but I'm not sure if anyone ha…

goseq gene ontology biomart annotate category

updated 8.3 years ago • krc3004

I've found myself in the situation where goseq fails with some relatively extreme numbers (derived from ChIP-Seq data with extreme changes in the IP target) and have

goseq

updated 3.5 years ago • Steve Pederson

<div class="preformatted">Hi, all I am trying to use goseq for RNAseq data analysis of a non-native bacteria, I fetch the genelength data and GO term data by using ensembl Perl API. Differential expression was done by DESeq2. After data run pwf of goseq, error occurred as following: ### Error in if (hi <= low) { : missing value where TRUE/FALSE needed Have any one met this befor…

RNASeq GO goseq DESeq2 RNASeq GO goseq DESeq2

updated 11.7 years ago • 刘鹏飞

Hello, I'm working recently on GO analysis regarding A.thaliana whose database is not included in GOseq package. Then I downloaded the GO annotation from both gene ontology website and TAIR as DAF file (version 2.0/2.1) and

goseq rnaseq r

updated 5.0 years ago • citronxu

I have a simple gene vector and trying to get the GO terms using the goseq package from Bioconductor in R. In this example just one gene:     > unique(d$genes\[1\])     > \[1\] "SMARCC1

R bioconductor gene ontology

updated 9.6 years ago • javier.mendoza

<div class="preformatted">Hello everyone This is my first message to Bioconductor, I hope someone out there can help me.?I have been working through the goseq vignette and adapting it to my own dataset. ?I have got my list of enriched go categories, which looks like this: > head(GO.wall...first message to Bioconductor, I hope someone out there can help me.?I have been working throu…

GO Category goseq GO Category goseq

updated 9.5 years ago • Helen Wright

I have some relatively small genes lists (around 10-20 significant genes (padj<0.05), and tried goseq to look for over represented GO terms and KEGG pathways. I also did the 'sampling' method as a negative control but this

goseq

updated 10.2 years ago • matt.arno

I am trying to install "goseq" Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2...I am trying to install "goseq" Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are the following please help me. ``` * installing *source* …

R Bioconductor Install

updated 2.9 years ago • abhisek001

HI, I'm getting following warning from `nullp` function from `goseq` package. ``` pwf=nullp(gene.vector1, bias.data=length.vec) Komunikat ostrzegawczy: W poleceniu 'pcls(G)': initial point very

goseq

updated 20 months ago • boczniak767

out (high scatter, poor fit). I have seen quite a few of these graphs when searching for "pwf plot goseq" on google including some on the bioconductor forum - but as yet there is no explanation for this.   Any ideas why this

goseq

updated 6.9 years ago • Jakub

myself in need of updating a lot of my > favorite packages. While trying to download and install goseq, from > source("http://bioconductor.org/biocLite.R") I received the following > notice: > biocLite("goseq") > BioC_mirror...bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.3. > Installing package(s) 'goseq' > Warnin…

GO rtracklayer goseq BiocInstaller GO rtracklayer goseq BiocInstaller

updated 13.5 years ago • Matthew Young

ensGene") > GO.hiper = goseq(pwf, "bosTau4", "ensGene") > GO.hiper[GO.hiper$category=="GO:0005509",] category over_represented_pvalue under_represented_pvalue...without categories in the test, the number of genes per category is the same! <pre> > GO.hiper = goseq(pwf, "bosTau4", "ensGene", use_genes_without_cat = TRUE) > GO.hiper[GO.hiper$category=="GO…

goseq biomart

updated 7.3 years ago • frezende

rownames(V16G16filt_lfc_up), rownames(V16V8filt_lfc_up)),]</pre> I want to subsequently perform GOseq analysis on this set (65 genes). Questions: 1.For GOseq, should my set of background assayed genes be all the genes assayed...count by summing exon lengths and calculating the median of transcripts per gene. Is this valid for GOseq? <pre> txdb <- makeTxDbFromGFF("../../Chi…

deseq2 goseq htseqcounts rnaseq plant

updated 9.4 years ago • Ben Mansfeld

div class="preformatted">Hi, I have a problem when working with GOSeq. There is support for mm10 genome but not Gene ID geneSymbol I am trying to get length information by following the Goseq

goseq goseq

updated 12.0 years ago • Thanh Hoang

Hi, I was having much trouble trying to install a goseq database in the annotation section. source("https://bioconductor.org/biocLite.R")   biocLite("org.Mm.eg.db") This...Hi, I was having much trouble trying to install a goseq database in the annotation section. source("https://bioconductor.org/biocLite.R")   biocLite("org.Mm.eg.db") This was...BiocInstaller 1.28.0)…

goseq org.hs.eg.db

updated 7.5 years ago • nancyjwahl7

Hi ALL, I have obtained a long list of GO terms in GOSeq. First, I would like to ask did GOSeq result can be used for analysis in REVIGO? if yes, should I input p-value or corrected

goseq revigo

updated 10.2 years ago • jackipchiho

Following on the question [here](https://support.bioconductor.org/p/80525/), but with a similar and yet slightly different problem: I am also using goseq with a manually compiled annotation, and am getting a strange plot similar to the one described by the author above (but...p/80525/), but with a similar and yet slightly different problem: I am also using goseq with a manually compiled annotat…

goseq

updated 9.3 years ago • Darya Vanichkina

div class="preformatted"> Hi everybody, I Have used goseq to take out the enriched GO-terms from my RNA-seq and microarray data and I want to visualize the output from goseq in a

Microarray Pathways Network goseq Microarray Pathways Network goseq

updated 13.0 years ago • Guest User

a few other related packages, I think). However, I've carried out GO/KEGG enrichment analyses using GOSeq so I can account for any potential sequence length biases. Is there a way to to use the various plotting functions with...data from other programs like GOSeq? Can we convert the results into the format required for ```emapplot()``` etc? The results for GOSeq, at least, are just stored in

clusterProfiler enrichplot

updated 4.5 years ago • charles.foster

Hi there, I am having problem loading or downloading genelendatabase for GoSeq package. I am using the latest R (Version 0.99.467). I never had any problem until I upgraded my R to version 3.2.1. Anyway...error message:  <span style="line-height:1.6">Error: package ‘geneLenDataBase’ required by ‘goseq’ could not be found</span>   <span style="line-height:1.6"&…

goseq genelendatabase

updated 10.2 years ago • FeiYian Yoong

I have been trying to generate GO category table for Chinese hamster genome using getgo function in goseq package. Even though chinese hamster is said to be included in the supportedGenomes() function of goseq, i am having trouble

GO Category goseq

updated 11.1 years ago • upendra kumar devisetty

managed to test for differential gene expression using "DESeq2" followed by GO-analysis with "goseq". So far, so good. However, I would like to know which genes (annotated to this pathway) are differentially expressed in my...dataset.   <pre> library(DESeq2) library(goseq) library(GO.db) library (org.Mm.eg.db) library(annotate)</pre> <pre> #"DESeq2": Pulling …

deseq2 goseq rnaseq go enrichment differential gene expression

updated 7.7 years ago • josef.oeckl

if there were plans to add the ability to account for gene length similar to how it's done in GOseq. Thanks, Julie Julie Leonard Computational Biologist Global Bioinformatics Syngenta Biotechnology, Inc. 3054 E. Cornwallis

goseq SeqGSEA goseq SeqGSEA

updated 9.9 years ago • Julie Leonard

using Trinity and RStudio and I am very new to all of this. I have a problem with the output of goseq. I get many GO terms in each category instead of getting one go term per category which is what I see in every paper. I believe...GO:1902494" "GO:1903046" "GO:1903293"</p> </td> </tr> </tbody> </table>     GO.wall=goseq(pwf, gene2cat = geneID2GO, …

go goseq goterm category

updated 7.2 years ago • Juan

reads were mapped to the genome build/version `sacCer3`. sacCer3 was released in 2014. I've tried `goseq`, which has built in support for sacCer2 but not sacCer3 (oy vey!). I was able to run my dataset using sacCer2, but **are GO Annotations...for sacCer2 in goseq up to date**? I've tried to make my own genome/object for use with goseq. I have a vector of gene names and lengths, but I canno…

clusterProfiler AnnotationDbi OrgDb goseq

updated 4.7 years ago • vanbelj

t get the link in the HTML page which is generated.   For example, if I want to refer to the goseq function in the goseq package, I type: <pre> #' @param x An object containing the data frame generated with \code{\link[goseq]{goseq

roxygen2

updated 9.4 years ago • b.nota

div class="preformatted">Hi, I want to do the GO analysis for Arabidopsis using GOseq package. From the PDF I understood that the package relies on the UCSC genome browser to extract information regarding

GO Category goseq GO Category goseq

updated 14.1 years ago • Divya, D.

different packages to compute GSEA for a given list of differentially expressed probe sets / genes (goseq, topGO, gega, gsea, GOstats...). In many cases, every method claims to be the best, and it's getting hard for me to choose a proper

GSEA goseq topgo gega gostats

updated 9.9 years ago • jacorvar

the current releases of databases. danRer6" is available and is not working for me. I am using GOSeq for gene ontology analyses and had the error as below:   <pre> Can't find danRer10/ensGene length data in genLenDataBase

genelendatabase goseq

updated 9.6 years ago • Mehmet Ilyas Cosacak

list, i need to get the length of genes in Arabidopsis thaliana in order to use the R package 'goseq'. Since Arabidopsis thaliana is not in the native 'goseq' database, I first tried to get a 'transcriptDb' object as suggested...in the documentation of 'goseq', with 'makeTranscriptDbFromBiomart' command from the 'GenomicFeatures' package. But I got the following error message

Arabidopsis thaliana biomaRt Arabidopsis thaliana biomaRt

updated 14.1 years ago • annaick.carles

using enrichment results that are contained in data.frames? For example, clusterprofiler vs goseq vs topGO. Thanks

clusterprofiler enrichment analysis

updated 8.8 years ago • fizer

bioinformatics work, which I hope someone can give me the answer and suggestions. I am try to use GOseq package to get GO enrichment for my data which is not built-in oraganism. >enriched.GO=unsorted_L14.15_S_GO.wall...0 405 0.5182944 Cucsa.000270 0 258 0.5205436 > unsorted_L14.15_S_GO.wall <- goseq(unsorted_L14.15_S_pwf, gene2cat=unsorted_L14.15_S_gene2g…

GO Category goseq GO Category goseq

updated 11.2 years ago • Guest User

for microarray data). The only gene set enrichment algorithm that I am aware of for RNA-Seq data is GOSeq, but it uses a competitive/gene sampling method (i.e. Fisher's Exact Test). Note, the ideas of self-contained vs competitive

Microarray goseq Microarray goseq

updated 13.5 years ago • Julie Leonard

Hello all, I've attempted to use GOseq, and while I know that, due to the gene length correction, it is more appropriate for RNAseq data than topGO, I like that...Hello all, I've attempted to use GOseq, and while I know that, due to the gene length correction, it is more appropriate for RNAseq data than topGO, I like that topGO...this matching method to pick genes with similar length I by that …

topgo goseq deseq2

updated 9.3 years ago • Ben Mansfeld

produced by via pathview (based on the functional enrichment results found using Clusterprofiler and Goseq) we are specifically asked to provide a permission for the usage of the figures,  since in the figures it is specifically

pathview clusterprofiler

updated 9.0 years ago • assaf www

div class="preformatted">Hi, Now I am want to use goseq for doing GO analysis of my bacteria RNA- seq data, but now I am stucked by the following issue: 1, makeTranscriptDbFromGFF...try to use it to build TranscriptDb in order to get the lengthData which needed to import into goseq >library(GenomicFeatures) >gffFile="/home/liupf/NC_009454.gff" >txdb <- makeTransc…

GO TranscriptDb goseq genomes GO TranscriptDb goseq genomes

updated 12.0 years ago • 刘鹏飞

f1000research.com/articles/5-1438/v2) until _Pathway analysis_ because I wanted to replace it by `` goseq ``. > head(gene_len) V1 V2 V3 1 Length GC NA 2 sp0000001 6406 0.3535748 3 sp0000002 333 0.5495495 4 sp0000003 216 0.4583333

edger goseq

updated 8.1 years ago • mictadlo

correcting for this bias by adopting the probability-weighting function (pwf) in the package goseq, that is more usually used to correct for gene-length bias in RNA-seq data.  It is straightforward to use this probability

goseq 450k enrichment

updated 10.6 years ago • Ed Schwalbe

hello I am a beginner who just started using rstudio (I just know how to make a Venn diagram in R). I tried to create a GO plot using usegalaxy, but they did not provide detailed plots for CC, BP, and MF (probably because my organism is not a widely known organism such as human or mouse). I have a goseq result file annotated as below. Is there anyone who can give me some help or com…

clusterProfiler ggpubr

updated 18 months ago • BCS12

Hi, I have done differential expression analysis with `DESeq2`. With `goseq` I can see there are pathways of interest differentially expressed- that makes sense to our biological observations

roast DESeq2 GeneSetEnrichment

updated 4.8 years ago • prabin.dm

try my luck with R - Bioconductor. I have heard of tons of tools supporting GO such as GO.db, topGO, goseq, GOstats, biomart etc... and I have been reading their description and examples, but honestly I am overhelmed and dont really

Transcription GO GOstats biomaRt topGO goseq Transcription GO GOstats biomaRt topGO

updated 14.6 years ago • Duke

Hi I am trying to build the organism package for sheep. At the first i used the codes that was in vignette help page. and so run makeOrgPackage. makeOrgPackage(gene\_info=fSym, chromosome=fChr, go=fGO, version="1.0.0", maintainer="Some One <so@someplace.org>", …

goseq

updated 7.2 years ago • Mehdi

to do a GO term enrichment analysis. How may I get the GO term for all of my genes using R package "goseq". I haven't found the database for soybean genome in bioconductor. Also online software like DAVID, shinyGo is not recognizing

GOTerm

updated 3.6 years ago • Afsana

Hi, I am having the same problem, but don't understand Naomi's solution. What is the DEgene vector supposed to be if not my de.gene list? Thank you for your help. best wishes, Chris Christopher Gregg, PhD. Assistant Professor, Neurobiology and Anatomy Adjunct Professor, Human Genetics 323 Wintrobe Bldg 530 University of Utah, School of Medicine 20 North 1900 East, 401 MREB Salt Lake City, Uta…

updated 13.9 years ago • Christopher T Gregg

Hi all, When creating pwf I encounter this type of message: > pwf <- nullp(genes, "hg19", "ensGene") Loading hg19 length data... Error in qr.R(qrx) : could not find symbol "..." in environment of the generic function I have tried to take a look into the matrix and it's basically composed of Ensembl IDs and 1-0 values accordingly to differentially and non differentially expressed genes.…

updated 12.4 years ago • Emanuela

an object with GO numbers (values), and their genes (ind) which is made from the getgo function from goseq: <pre> all23kGos <- stack(getgo(assayed.genes,'hg19','geneSymbol')) sorted<-all23kGos[order(all23kGos$values),] > tail(sorted

goseq sink cat print

updated 9.7 years ago • b.nota

I have trouble getting the goseq package to work. I am using R-3.3.0; and have installed goseq version 3.5; as well as the "org.Hs.eg.db" package. Unfortunately...I have trouble getting the goseq package to work. I am using R-3.3.0; and have installed goseq version 3.5; as well as the "org.Hs.eg.db" package. Unfortunately I don't get goseq functions to work:   Example: ensgenes&am…

rnaseq goseq package installation

updated 8.4 years ago • sr17

I maintain "rgsepd" which uses "DESeq2" and "goseq" to run an annotation pipeline. Internally, when I have a character representation of a GO term I'm interested in more...I maintain "rgsepd" which uses "DESeq2" and "goseq" to run an annotation pipeline. Internally, when I have a character representation of a GO term I'm interested in more information

GO.DB

updated 7.4 years ago • karl.stamm

<div class="preformatted">Hi Yemi, I have posted recently an updated version of SPIA (2.10.0) (available in the devel branch) that you can use to run SPIA on any organism available in KEGG starting with KEGG KGML files. It seems that there is a KEGGREST package from the bioc team that can help you get those files. Below are a few lines that I borrowed from Dan Tenenbaum showing how to get …

Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST

updated 12.6 years ago • Tarca, Adi

#!/usr/bin/env Rscript # based on https://www.biostars.org/p/84467/#84495 # source("https://bioconductor.org/biocLite.R") # biocLite("GenomicRanges") # biocLite("rtracklayer") biocLite("Rsamtools") library(GenomicRanges) library(rtracklayer) library(Rsamtools) GFFfile = "Sp.gff" FASTAfile = "Sp.faa" #Load the annotation and re…

goseq

updated 8.1 years ago • mictadlo

nbsp; I am trying to build the goseq db for Mycoplasma hyorhinis.  Here is what I used: makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer

AnnotationForge

updated 9.9 years ago • songeric1107

<div class="preformatted">1) Is RNA-Seq data even appropriate for "standard" cluster analysis due to its discrete nature? What normalization should be done beforehand? We tend to perform length and TMM normalization of our data. 2) If we perform some sort of clustering of RNA-Seq data, and then obtain a gene list from a cluster (e.g. all genes in a cluster) and then want to perform gene …

Normalization Clustering Normalization Clustering

updated 13.5 years ago • Julie Leonard

we have difficulties to find an optimal method to do this. We tried several packages (e.g gage, goseq) and web-based softwares (e.g GeneGO, AmiGO) and found different outputs (sometimes opposite results). What could be the

GO gage goseq KEGG

updated 11.0 years ago • Merienne Nicolas

I am trying to make db for Mycoplasma genus = "Mycoplasma", species = "hyorhinis", but I get error, could you please help. makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer = "me <me@mine.org>", outputDir = ".", tax\_id = "1129369", genus = "Mycoplasma", species = "hyorhinis", NCBIFilesDir = ".") cache will try to rebuild once per day. Getting data for gene…

go

updated 9.8 years ago • songeric1107

Hi, Do you have any ideas? I have converted gene names many times, but still does not fit, same problem... -- output of sessionInfo(): Loading hg19 length data... Error in getlength(names(DEgenes), genome, id) : The gene names specified do not match the gene names for genome hg19 and ID knownGene. Gene names given were: uc002qsf.2, uc002qse.3, uc009xov.3, uc021rmd.1, uc001qvk.1, uc…

updated 13.0 years ago • Guest User

cruk-summer-school-2018/RNASeq2018/html/06_Gene_set_testing.nb.html#go-enrichment-analysis in the goseq package. The code to make this plot taken from the site is the following: ```r goResults %>% top_n(10, wt=-over_represented_pvalue...in the R documentation. Will the way I have written the plot give an analogous output as the goseq package? The output from gage is p.geomean,stat.me…

gage plot RNASeq goseq

updated 3.6 years ago • m.glymenaki

RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund")) to install

microarray software error bioconductor

updated 10.0 years ago • o.j.james

Hi, I am getting the following error when running nullp Error in if (min(fv) < lower\_bound) fv = fv - min(fv) + lower\_bound : missing value where TRUE/FALSE needed I've traced the problem to makespline.R line 53. pcls(G) is return NaNs. FYI, line 17 (if(hi<=low) {) is true so the reflection occurs. If I change the nKnots parameter from 6 to 7, there ar…

software error

updated 10.6 years ago • suzy.stiegelmeyer@syngenta.com

girafe); ChIP-seq (BayesPeak, CSAR, PICS, tigre); digital gene expression and RNA-seq (DESeq, goseq, segmentSeq); and motif discovery (MotIV, rGADEM). Microarray analysis includes new packages for pre-process and technology...Alignments for Functional Exploration http://bioconductor.org/packages/2.6/bioc/html/girafe.html 19. goseq Gene Ontology analyser for RNA-seq and other length biased data …

Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa

updated 9.1 years ago • Patrick Aboyoun

<div class="preformatted">Dear Gordon, Thank you very much for your detailed explanations and clarifications. Very useful. Thanks, Paolo -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Saturday, April 28, 2012 22:38 To: Paolo Guarnieri Cc: Bioconductor mailing list Subject: gene set enrichment analysis of RNA-Seq data Dear Paolo, Well, first of all, let…

Microarray limma GLAD edgeR goseq Microarray limma GLAD edgeR goseq

updated 13.4 years ago • Paolo Guarnieri