Bioconductor Forum

database documentation, the bioconductor mailing list, the > BSgenome documentation, and the goseq documentation, I am still very > confused about whether I can use the assembly 4 package that Herv? > posted in goseq...Just to clarify, goseq is not my package so I can't "post" anything in it, whatever that means. I assume you are talking about the BSgenome.Amellifera.BeeBase.…

Annotation GO Cancer BSgenome Biostrings BSgenome rtracklayer GenomicFeatures goseq GO

updated 12.2 years ago • Hervé Pagès

I’m currently attempting to perform an analysis using GOseq on the up regulated genes of a RNAseq experiment. The thing is I keep getting a plot as the one I attached

goseq

updated 8.6 years ago • dlsoltero

Hi all,   I am trying to install goseq as specified [here. ](https://bioconductor.org/packages/release/bioc/html/goseq.html) This is the commands I put in: R source...https://bioconductor.org/biocLite.R") biocLite("goseq") At the end of the installation, it prints this: The downloaded source packages are in       &n…

goseq installation

updated 6.4 years ago • philipp.voss

I have followed this [tutorial](https://f1000research.com/articles/5-1438/v2) for edgeR. On this [side](https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=f599adf23b671cad&tool_config=%2Fsrv%2Ftoolshed%2Fmain%2Fvar%2Fdata%2Frepos%2F002%2Frepo_2703%2Fgoseq.xml&changeset_revision=ade933eff007) it appears I could run `` goseq `` when I have created the following fil…

edger goseq

updated 6.6 years ago • mictadlo

Hello all, I am encountering problems with the goseq package. I did some analysis few months ago without any problems and I now need to reuse the script for another part of...inequality constraints</pre> Because I updated my Bioconductor packages recently (I think I used goseq\_1.16.2 before) and I am using an old R version (still the one for Snow Leopard), I am thinking that it could be …

goseq RNAseq mm10

updated 8.9 years ago • Merienne Nicolas

for you to use a genome which is not supported (if it's not in UCSC then it's not supported in goseq) then you are right in that you will need the annotation (gene length) and the mapping from geneids to GO terms. It's not enough...just to have the genome in order to use goseq. Cheers, Alicia On 25/02/12 6:32 PM, "bioconductor-request at r-project.org" <bioconductor-request at="" r-project.…

Annotation GO Cancer Apis mellifera BSgenome Biostrings BSgenome rtracklayer goseq GO

updated 12.2 years ago • Alicia Oshlack

I have successfully conducted a gene ontology analysis using goseq. In presenting the findings of the analysis (i.e., the standard output generated by the \`goseq\` function) to a colleague, he...function were those associated with any given significant GO or KEGG term arising as output of the \`goseq\` function. The columns \`numDEInCat\` and \`numInCat\` clearly summarize this information (i.e…

goseq gene ontology

updated 6.5 years ago • JMallory

Hello, I've tried to install the package goseq with: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("goseq") But...R/library/geneLenDataBase’ ERROR: dependency ‘geneLenDataBase’ is not available for package ‘goseq’ * removing ‘/usr/local/lib64/R/library/goseq’ The downloaded source packa…

goseq r package r

updated 4.6 years ago • Raito92

img alt="" src="http://i.imgur.com/K8MzXPo.png" style="height:504px; width:504px"/> Hi, I use goseq and with the Wallenius approximation I get 264 BH adjusted significant overrepresented categories, with the sampling

goseq

updated 8.9 years ago • idomtamir

Hi, I've been following the vignette, but I keep getting the following error with supportedOrganisms() from goseq: __Error in matrix(unlist(pairs), nrow = 2) :   'data' must be of a vector type, was 'NULL'__ Is there something I am doing wrong? Many thanks in advance!! Victoria R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch" Copyright (C) 2016 The R Foundation for…

go goseq

updated 7.1 years ago • starbug16

I'm getting a warning message when I try to run Gene Ontology analysis with *goseq* using human genome assembly GRCh38 (hg38). I know that hg38 isn't natively supported by *goseq*, but *goseq* will fetch *goseq...installed. Thus, I run the following code: ``` library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(goseq) # load toy dataset aa = c(1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1) names(aa) …

goseq

updated 3.2 years ago • Nikolay Ivanov

Hi, I have a microarray data that I would like to do GO analysis using GOSeq. However, I have ENTREZ gene ids. When I am trying to convert ENTREZ ids to ENSEMBL ids, I lose several of my genes from the

goseq entrez gene identifiers

updated 8.0 years ago • Mehmet Ilyas Cosacak

s fine. While well represented in the literature, I'm wondering if this approach is not redundant? GOseq is supposed to prevent biases introduced by the greater power to detect DE in longer transcripts. However, since the...have effectively compensated for any gene length effects, it seems like the subsequent use of GOseq could result in more false <s>positives </s>&nbsp…

deseq2 goseq gene ontology differential gene expression

updated 6.8 years ago • david.rinker

which are ensembl Ids I wanted do GO analysis for this list of genes. How can I do this from the GOseq I went through vignette which is running the GOseq from the DE genes output, my genes list are not from the DE this are obtained

goseq

updated 3.1 years ago • Lucky

nbsp; Anyone has some advice on how to get it running?  Thank you,   > library(goseq) Indlæser krævet pakke: BiasedUrn Indlæser krævet pakke: geneLenDataBase Error: package or namespace load failed...goseq’ in loadNamespace(j <- i\[\[1L\]\], c(lib.loc, .libPaths()), versionCheck = vI\[\[j\]\]):  der er ingen pakke med navn ‘GO.db’ > so…

GO.db goseq package installation error

updated 6.6 years ago • veerle

writing because of some warnings that appeared when running the _nullp_ command. It seems GOseq cannot find the gene lenghts for my data ('hg38','ensGene') in genLenDataBase. I installed the TxDb.Hsapiens.UCSC.hg38.knownGene

goseq

updated 7.6 years ago • webquelzinhablue

Following the instructions on https://bioconductor.org/packages/devel/bioc/vignettes/goseq/inst/doc/goseq.pdf To see what genomes are in the local database, I am told to type: __supportedOrganisms()__ ...which returns...GenomeInfoDb\_1.6.3__ __\[10\] IRanges\_2.4.8 S4Vectors\_0.8.11 BiocGenerics\_0.16.1__ __\[13\] goseq\_1.22.0 RSQLite\_1.1-2 geneLenDataBase\_1.6.0__ __\[16\] BiasedUrn\_1.0…

goseq unsupported organisms supportedgenomes supportedorganisms error

updated 7.1 years ago • tootiki

<div class="preformatted"> Hi all and M. Carlson I am now working on an archaea, which is not a common organism. I want to use goseq to do the GO analysis of my RNAseq data.In order to creat the category mappings(relationship between GO and gene id), I...Hi all and M. Carlson I am now working on an archaea, which is not a common organism. I want to use goseq to do the GO analysis of my RN…

RNASeq GO Organism AnnotationDbi goseq RNASeq GO Organism AnnotationDbi goseq

updated 10.5 years ago • 刘鹏飞

Hello Sir, I am using it for non-model organisms. 1) I have a set of differentially expressed genes, plus the go term related to genes. 2 ) The command in R in need to use is: goseq(pwf, genome, id, gene2cat = Null) I understand that for gene2cat argument I need to mention my list of genes with their go term.Correct...expressed genes, plus the go term related to genes. 2 ) The command in…

annotation goseq

updated 3.9 years ago • kumararya563

differentially expressed genes checked for over-reppresentation using the procedure available in the goseq package. The topGO package (see, for example, the chapter 7.4 of the included vignette) allows this kind of visualization...data. Any idea how this kind of visualization can be produced for RNAseq data inspected using goseq? Any idea would be appreciated! Regards, Paolo [[alternat…

Microarray GO Visualization Microarray GO Visualization

updated 13.1 years ago • Paolo Sonego

div class="preformatted">Dear Matthew, I am getting the following error when using goseq. Any idea what may cause it? Thanks, Adi > pwf=nullp(genes,bias.data=cntbias) > gocats=as.list(org.Hs.egGO2ALLEGS) &gt...GOr=goseq(pwf,gene2cat=gocats) Using manually entered categories. Calculating the p-values... Error in dWNCHypergeo(num_de_incat

GO goseq GO goseq

updated 11.1 years ago • Tarca, Adi

on the following error. It's generated when I attempt to access the supported organism list in goseq.  __> supportedOrganisms()__ __Error in getNodeSet(doc, "//table\[@class='descTbl'\]")\[\[1L\]\] :    subscript out of bounds__

goseq

updated 7.1 years ago • jesykamelendez

Hi All, I am using GOseq as part of the Trinity pipeline to perform gene ontology testing for genes in a _de novo_ transcriptome assembly...Hi All, I am using GOseq as part of the Trinity pipeline to perform gene ontology testing for genes in a _de novo_ transcriptome assembly. I used edgeR to perform DGE analysis comparing groups that were treated with a che…

goseq go enrichment

updated 5.8 years ago • mart1139

Hello everyone, I am new to this forum so I'm apologizing in advance if I am not posting in the most formal way. I am using the goseq package from bioconductor in order to perform enrichment for markers that are differentially methylated (limma output). These markers have been measured  according to CpG arrays from 450K illumina (i.e. cg07790169) and I am retrieving them on uc…

goseq methylation ensembl ucsc limma

updated 6.1 years ago • dusan.petrovic

r-project.org Subject: Re: [BioC] Visualising the GO structure (RNA-seq) using topGO and goseq Message- ID: <4D9270E1.1000303@fhcrc.org> Content-Type: text/plain Hi Paolo, Not quite sure what you want from your...expressed genes checked for > > over-reppresentation using the procedure available in the goseq package. The > > topGO package (see, for examp…

Microarray GO Visualization graph topGO goseq Microarray GO Visualization graph topGO

updated 13.1 years ago • Paolo Sonego

Recently I started using it for pathway analysis. It works well for human mRNAseq DGE data. But I encountered some problem with non-model samples. I hope I could get some help from you. The specific problem I have is with cat genome. I looked up the supported genome: > supportedGenomes()[,1:4] <code>12 felCat5 Cat Sep. 2011 ICGSC Felis…

goseq genesetenrichment annotation

updated 8.7 years ago • xyliu00

The vignette of GOseq details in section 6.8 how to correct for total read count bias (per gene). The code used to calculate total read

Coverage goseq

updated 7.0 years ago • Christopher Conley

I did the GO terms enrichment analysis using GOSeq, after that I want to access the esIDs in the significantly enriched terms. I tried to extract esIDs using `` org.Hs.eg.db...in `` GO.wall `` report is 124, so is there any method to directly access the genes in GO terms in GOSeq

GOseq ensemblid GO

updated 5.4 years ago • mico

Hello there, I have a question concerning usage of GOseq for testing custom gene list (approx. 1k genes) enrichment. I am not sure about the `use_genes_without_cat` argument value

goseq

updated 5.2 years ago • kubovcij

of mac. Thanks in advance, Steve > source("http://bioconductor.org/biocLite.R") > biocLite("goseq") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.7. Warning: unable to access index...http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .15 Installing package(s) 'goseq' Warning: unable to access index for repository http://li…

BiocInstaller BiocInstaller

updated 11.8 years ago • steve Shen

I am suddenly having trouble using goseq for supportedOrganisms as bioconductor suddenly seems unable to retrieve the appropriate data from the UCSC database

goseq Bioconductor rtracklayer

updated 6 weeks ago • thomas

Hi! Does the goseq package always use the most current release of an Ensembl genome or is it possible it may be using previous archives

goseq ensembl

updated 8.1 years ago • mrodrigues.fernanda

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...package that corresponds to the relevant entry in the list. To access this variable type: > goseq:::.ORG_PACKAGES anoGam Arabidopsis bosT…

Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO

updated 12.1 years ago • Matthew Young

Hi Guys Here I am again with another question about goseq. I am following the goseq tutorial. I am manually inserting my length and go data, since the combination o fmy species genome...and gene ID is not supported by goseq.  I ran the following code, and it ran fine as you can see in my output: <code>GO.wall <- goseq(pwf, gene2cat = Biomart.GOdata...categories in the ca…

goseq

updated 8.0 years ago • mrodrigues.fernanda

Hi, I am thinking about switching from GoStats to GoSeq. Is there a built in possibility to use the ENSEMBL transcript annotation or can I only use ENSEMBL genes? Do I have to...Hi, I am thinking about switching from GoStats to GoSeq. Is there a built in possibility to use the ENSEMBL transcript annotation or can I only use ENSEMBL genes? Do I have to annotate

goseq ensembl

updated 8.9 years ago • idomtamir

over representation) analysis of GWAS/QTL data distributed over a genome, is it possible with goseq?  I could not find any useful tutorials/manual -- could someone kindly show (1) required inputs (format, etc.; e.g. we have...coordinate locations", "a small segments of a genome region to test"), (2) command line to run R/goseq (so that we can build a pipeline to run as routine), and (3) …

goseq enrichment GWAS

updated 5.7 years ago • zhu

I am trying to run goseq package in R, working with human data with hg19. I followed the vignette instructions to create "gene.vector", but I am...I am trying to run goseq package in R, working with human data with hg19. I followed the vignette instructions to create "gene.vector", but I am getting

goseq GO term

updated 6.6 years ago • pereyra.s

Has anyone else encountered any issues with using mm10 in the goseq package: <pre> > pwf <- nullp(genes, "mm10", "geneSymbol") Can't find mm10/geneSymbol length data in genLenDataBase... Found the

goseq

updated 8.2 years ago • Bohdan Khomtchouk

Recently, I have tried to apply GOSeq to RNA-seq expressions after voom adjustment. It has just ocurred that differential expression and gene length were

limma limma-voom goseq

updated 6.2 years ago • joelrosa

Hi all,  I am using goseq to correct for RNA-seq length bias. Since my dog genome (canFam3) is not supported in goseq database, I tried to make TXDb...nbsp;  __If it's correct, it could potentially be a tutorial and benefit other users since the goseq documentation isn't very self-explanatory.  __ I have posted a question in BioStars but I think I could potentially..…

deseq2 goseq biomart r rnaseq

updated 8.0 years ago • CandiceChuDVM

nbsp; Dear all, I am running GOseq on a custom annotated dataset. I am getting a nicely looking output: list of enriched and depleted GOterms for my different

GOseq GO pwf goseq

updated 5.7 years ago • TB18

Relevant sessionInfo(): R version 3.2.2; BiocInstaller\_1.18.4 ; goseq\_1.20.0 I am relatively new to R and to Bioconductor packages. I am using goseq for GO enrichment analysis of mouse RNA...GO term enrichment analysis despite their NA pwf values? (5) I'm assuming that at this stage in the goseq pipeline the NAs have nothing to do with whether the genes have GO annotations, correct? (I cannot …

goseq pwf

updated 8.6 years ago • mjnolte

resolve __length bias__)__:  __ Since the dog genome assembly canFam3 is not supported in goseq database, I have to make my own \`bias.data\` to perform \`nullp\` in goseq. I was able to perform \`GO.wall=goseq(pwf,gene2cat...bias into consideration. However, "limiting GO categories and other category based tests" as \`GO.MF=goseq(pwf,gene2cat=geneID2GO, test.cats=c("G…

rna-seq limma goseq

updated 7.9 years ago • CandiceChuDVM

Hi, I've performed KEGG pathway analyses using the GOseq package and now I was wondering how do I know which genes were included in the "numDEInCat"? See below for example:&nbsp...Hi, I've performed KEGG pathway analyses using the GOseq package and now I was wondering how do I know which genes were included in the "numDEInCat"? See below for example:  <table...find anything reg…

GOseq KEGG

updated 7.3 years ago • Xavier

Hi! I am using goseq on some bovine data and I am using Ensembl IDs for bovine genome UMD3.1, which is not supported by goseq, so I had to input

goseq

updated 8.0 years ago • mrodrigues.fernanda

Hi, I've performed gene ontology analysis with GOseq using the standard ontologies, as well as using KEGG and Reactome. When using the default ontologies or KEGG, the function

goseq go rna-seq

updated 4.0 years ago • hasse.bossenbroek

pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How to solve that as I am not sure what the...error means? ```r library(goseq) supportedOrganisms() %>% filter(str_detect(Genome, "hg")) #Step 1 #prepare the results for goseq de.genes&am…

Pathways goseq RNASeqData

updated 2.1 years ago • m.glymenaki

was also performed through the analyze_diff_expr.pl script. The function calls the R package **goseq**, and [as stated here][2], the output looks this way: *Two outputs will be generated for each set of genes tested for functional...Trinity-Differential-Expression [2]: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-GOSeq [3]: https://i.ibb.co/WDvmhxb/41390-2018-192-Fig3-HTML…

go enrichment gene ontology goseq go

updated 4.6 years ago • Raito92

div class="preformatted">Hi, I have got an error while i have been running goseq R package using UCSC known gene ID such numbers, 1,2,...27315.(27181 genes). When i computed pwf. it was fine. but, In getgo function

GO goseq GO goseq

updated 14.0 years ago • sunghee OH

div class="preformatted">Hello, I've been trying to install goseq on R-2.15.2 but one of the dependencies, RCurl is not installing. I've compiled curl and curl-config (7.28.0); there is also

goseq goseq

updated 11.5 years ago • Dave Tang

Hi, I'm running pathway analysis with goseq but had the error : In pcls(G) : initial point very close to some inequality constraints : when plotting the nullp. I'm...Hi, I'm running pathway analysis with goseq but had the error : In pcls(G) : initial point very close to some inequality constraints : when plotting the nullp. I'm not

goseq warning message pwf mgcv

updated 6.7 years ago • heikki.sarin

Hello I got this error when using supportedGenomes() in goseq package: <pre> > library(goseq) Loading required package: BiasedUrn Loading required package: geneLenDataBase > head

goseq rtracklayer

updated 6.5 years ago • mgdrnl

div class="preformatted"> Hello, I performed an analysis with EdgeR followed by an analysis with GoSeq and then I got this error message, saying there is an error in if (matched_frac == 0) { :missing value where TRUE/FALSE is required

edgeR edgeR

updated 11.4 years ago • Guest User

there are now two copies of curl and curl-config (the old and new version). I will just do the goseq analysis on my own Ubuntu box. Thanks again for your help, Dave </dtenenba></davetingpongtang></dtenenba></mtmorgan></div

goseq goseq

updated 11.5 years ago • Dave Tang

Hi! I am trying to use the package goseq, but when I try running the function supportedOrganisms() R says it cannot find it. Does anyone know what might be the reason...grDevices utils \[7\] datasets methods base other attached packages: \[1\] KEGG.db\_3.2.2 goseq\_1.22.0 \[3\] geneLenDataBase\_1.6.0 BiasedUrn\_1.07 \[5\] GOstats\_2.36.0 graph\_1.48.0 \[7\] Category\_2.36.0 GO.db\_3.…

goseq

updated 8.1 years ago • mrodrigues.fernanda

sum(exonBaseMean), sig = max(sig) ) %>% ungroup() I can then run goseq using  the lengths as the bias data: genes <- retained_genes$sig names(genes) <- retained_genes$gene_id bias.data...CY9MhRQ.png) And then proceed to test for category enrichment: go.retainted.length <- goseq(pwf, genome='hg19',…

goseq dexseq

updated 6.7 years ago • i.sudbery

biocLite.R")Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help> biocLite("goseq")'BiocInstaller' package not in repository http://bioconductor.org/packages/2.11/bioc, using 'http://bioconductor.org

updated 11.4 years ago • Abhishek Pratap

  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 6.8 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 24 months 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 10.2 years ago • 刘鹏飞