192 results • Page 1 of 4
div class="preformatted">Hi , I have tried to run GOseq on my differential expressed gene list, but when I try to run the following command: GO.wall <-goseq(DEGgenes, pwf, "bosTau4
updated 13.1 years ago • Biase, Fernando
div class="preformatted"> Dear All: I have a question about the bioconductor goseq (http://www.bioconductor.org/packages/release/bioc/html/goseq.html) package for GO enrichment analysis (taking length...Those top-ranked categories are obtained based on the ranking of "over_represented_pvalues" from the goseq object. The goseq also includes "under_represented_pvalues" from the same output. Can…
updated 12.8 years ago • Gu Mi
div class="preformatted">Hi All, Using goSeq to analyze two gene lists - up regulated and down regulated genes generated with edgeR, the up regulated list seems good...lateTrans524.up.vector, bias.data=hs.glen.assayed, plot.fit=FALSE) > lateTrans524up.goWall <- goseq(lateTrans524up.pwf, gene2cat=hs.go, test.cats=c("GO:CC", "GO:BP", "GO:MF")) Using manually entered categories. Ca…
updated 12.4 years ago • steve Shen
div class="preformatted">Dear all, I am trying to analyze RNA seq data with goseq but I have a problem: mm10(the reference genome that I am using for my experiment) is not supported by goseq. The last version...supported by goseq is mm9. Can you help me to annotate mm10 RNA seq data with goseq? The version of my goseq is: 1.8.0. Thanks in advance. Regards
updated 11.2 years ago • Vincenzo Capece
div class="preformatted"> Dear all, I am using GOseq on a list of diffentially expressed genes and I would like to do an analysis at a specific GO level (level 4 for example...instead of the complete GO. Is there a tool in GOseq that already does it ? Or do I have to prepare the file for the gene2cat option by myself ? A somewhat similar question is...how to use the GOslim ontologies (a subse…
updated 10.0 years ago • amandine.fournier@chu-lyon.fr
of Bioinformatics, University of Georgia, USA. I have been trying to use the bioconductor package goseq for go- term/pathway enrichment of my expression data. Since my organism of interest isn't included in the goseq database...frame and list formats as specified. While the 'nullp' function worked fine for my data, when I run goseq() with the following command, I get an error message: > e…
updated 13.6 years ago • Joydeep Mitra
div class="preformatted">Hi Goseq ers, I followed the user manual for Goseq and came up with the following plot, I am working with corn data, so I imported the
updated 12.1 years ago • Alpesh Querer
<div class="preformatted"> Hi All, I've used the GoSeq package in R without any problem but I just wanted to know whether there is a way to know which genes mapped to each of the...div class="preformatted"> Hi All, I've used the GoSeq package in R without any problem but I just wanted to know whether there is a way to know which genes mapped to each of
updated 10.9 years ago • Guest User
div class="preformatted">Hi all, Our RNA-seq pipeline uses GOseq, and we are thankful to the authors for offering this great tools. GOseq crashed on us today on C. elegans data with the error...yeast org package. So for fun I listed all other genomes for which that would not work: library(goseq,quietly = TRUE) genomes = sort(supportedGenomes()$db) .ORG_PACKAGES = goseq:::.ORG_PACKAGES sup…
We are trying to use goseq on our yeast data, but there is a problem with the yeast database. I managed to create a pwf object with nullp(), but the next...LSR1 0 1175 0.06094949 NME1 0 340 0.03602508 &gt; GO.wall = goseq(pwf, "sacCer3", "ensGene") Fetching GO annotations... Error in toTable(get(paste(orgstring, "GO2ALLEGS", sep = ""))) : error in evalua…
updated 9.1 years ago • M.Gierlinski
div class="preformatted">I am thinking of using GOseq to obtain enriched GO terms for RNA-Seq clustering results. I plan to transform the RNA-Seq data before running clustering...to make it homoskedastic. When running GOseq, I would provide the list of genes that cluster together as the list of "DE genes". Question: Is this an appropriate usage...of GOseq? Or can/should I just use a standar…
updated 12.0 years ago • Julie Leonard
div class="preformatted">Dear All, Appreciate your time. Need your expertise. I am trying to use GOSeq for GO analysis of my RNA-seq experiments. I was using Tophat-&gt;Cufflinks for DE, and mouse mm10 for annotation. I am trying...to build the gene length database by myself, given that the current version of goseq does not support the mm10 build. 1, Cufflinks seems ignored the origina…
div class="preformatted"> Dear All, Appreciate your time. Need your expertise. I am trying to use GOSeq for GO analysis of my RNA-seq experiments. I was using Tophat-&gt;Cufflinks for DE, and mouse mm10 for annotation. I am trying...to build the gene length database by myself, given that the current version of goseq does not support the mm10 build. 1, Cufflinks seems ignored the origin…
Dear goseq developers! I was wondering whether there are any plans to implement the conditional test from the `` GOstats `` package...also in `` goseq ``? That test was pretty handy to not get all these very general GO terms being significant. cheers, jo
updated 8.7 years ago • Johannes Rainer
testing. When I look at the man page for goseq, it says: "test.cats A vector specifying which categories to test for over representation amongst DE genes. See details...a workshop I'm teaching on Thursday, and hope to find a quick answer! Thanks, Jenny &gt; library(goseq) &gt; &gt; library(edgeR) &gt; table.summary &lt;- read.table(system.file("extdata", "Li_sum.txt", p…
div class="preformatted">Hello List I'm using GOSeq to examine the biology behind genes found to be regulated in a RNA-Seq study. One of my comparisons yields ~450 regulated...genes. Attempting to run GOSeq with this list results in the following error: Error in if (min(fv) &lt; lower_bound) fv = fv - min(fv) + lower_bound : ? missing value
updated 12.1 years ago • Iain Gallagher
class="preformatted"> Hi Alicia: Thanks for your detailed reply! I have another question for the goseq method as stated below. I notice in the paper (http://genomebiology.com/2010/11/2/R14) of Young et al. (2010) that, for the category...GO:0016020 "Membrane", it ranks 1st using GOseq for total read counts adjustment (Table 4), while it ranks 702nd using GOseq for length bias adjustment (Tab…
updated 12.8 years ago • Gu Mi
<div class="preformatted">Hi Steve, This is not an error I've encountered before, so I don't know what the problem is off the top of my head. The error message makes me guess that the PWF is returning weird values (outside of the (0,1) range) for a couple of genes. Could you either send me the variables you used as input or try looking at the PWF p-values for the down list and see how th…
Hello, I use GOseq quite often for RNAseq analyses, including the length bias correction. My question is how to use it properly for data...pre> pwf &lt;- nullp(gene.vector, "hg19", "geneSymbol", bias.data = lengthhg19) GO.wall &lt;- goseq(pwf, "hg19", "geneSymbol", use_genes_without_cat = TRUE) </pre> But what to change for microarray data? Would it be enough to add...meth…
updated 8.2 years ago • b.nota
gt; To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> &gt; Subject: [BioC] GOSeq error &gt; Message-ID: &gt; &lt;1328880137.28802.YahooMailNeo at web86706.mail.ird.yahoo.com&gt; &gt; Content-Type: text...plain; charset="iso-8859-1" &gt; &gt; Hello List &gt; &gt; I'm using GOSeq to examine the biology behind genes found to be regulated in a &a…
updated 12.1 years ago • Alicia Oshlack
div class="preformatted">Unlike GOstats, goseq does not seem to allow a gene universe. Wouldn't it make more sense to compare the DE genes to all the genes that express
updated 13.0 years ago • Naomi Altman
text/plain &gt; &gt; Hi All, &gt; &gt; Using goSeq to analyze two gene lists - up regulated and down regulated &gt; genes generated with edgeR, the up regulated list seems...gt; bias.data=hs.glen.assayed, plot.fit=FALSE) &gt;&gt; lateTrans524up.goWall &lt;- goseq(lateTrans524up.pwf, gene2cat=hs.go, &gt; test.cats=c("GO:CC", "GO:BP", "GO:MF")) &gt; Using man…
I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories...I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories other than the GO categories. Specifically, I wanted to make use of the molecular signatures database (MSigDB). To be clear, …
updated 5.5 years ago • Mthabisi Moyo
I'm running goseq on a sequence of bootstraps where a DE test is performed on a random selection of replicates. THis way, I have a constant...genes and a selection of significant genes which is slightly changing from bootstrap to bootstrap. goseq works nicely on most of these bootstraps, but every now and then it crashes. Here is an example: <pre> &gt; library(goseq) &gt; library…
updated 9.1 years ago • M.Gierlinski
Alpesh Querer <alpeshq@gmail.com> &gt; &gt; To: bioconductor@r-project.org &gt; &gt; Subject: [BioC] Goseq plot &gt; &gt; Message-ID: &gt; &gt; <cao0xdqpci- dntu+yckafuf6h5wdjofj954ot+ktrto_ngu="xFA@mail.gmail.com"> &gt; &gt; Content-Type...text/plain &gt; &gt; &gt; &gt; Hi Goseq ers, &gt; &gt; &gt; &gt; I followe…
div class="preformatted">Hello, In the vignette (17th March 2012) of the goseq package (page 6), a list of differentially expressed genes produced by edgeR is used as input into goseq. However if I were...input genes that have a POSITIVE or NEGATIVE fold change (with an adjusted p-value &lt; 0.05) into goseq? It sounds obvious, but I'm not sure. Also I have some questions regarding the g…
is running Debian 10 with the default version 3.5.1 of R. I need to use the Bioconductor package "GoSeq" to perform functional enrichment tests as described in “Running GOSeq” pipeline (https://github.com/trinityrnaseq/trinityrnaseq...wiki/Running-GOSeq). I got a trouble with it. The package "GoSeq" exists only for “R version "3.6" in Bioconductor Release 3.10 which works with...https://communi…
updated 4.2 years ago • gdalsky
C stack usage&nbsp; 7969392 is too close to the limit ERROR: lazy loading failed for package ‘goseq’ \* removing ‘/home/biosys5/R/x86\_64-pc-linux-gnu-library/3.4/goseq’ The downloaded source packages are in &nbsp;&nbsp; &nbsp;‘/tmp...message: In install.packages(pkgs = doing, lib = lib, ...) : &nbsp; installation of package ‘goseq’ had non-zero exit status So…
updated 6.0 years ago • TB18
<div class="preformatted">Dear R helpers, I've been successfully using Goseq to measure GO and KEGG enrichment in diverse RNASeq experiment. I was wondering if is there any way to use different datasets...div class="preformatted">Dear R helpers, I've been successfully using Goseq to measure GO and KEGG enrichment in diverse RNASeq experiment. I was wondering if is there any way to use di…
updated 9.7 years ago • Eduardo Andres Leon
Dear goseq developers and all, Following the question here https://support.bioconductor.org/p/60759 The code in Goseq manual says
updated 7.6 years ago • assaf www
Dear all, I have carried out differential expression of RNA-seq data from a non-model organism using the limma+voom pipeline. Next, I wish to look for functional enrichment of DE genes using GOseq. I successfully used GOseq on my data set by following the GOseq vignette, using custom gene lengths and GO mappings. However, I note that following the vignette leads to **all** DE genes being t…
updated 4.9 years ago • charles.foster
div class="preformatted">Hi all, I'm using goseq for the analysis of DE genes from and RNA seq dataset-I've only recently started using R however &amp; am fairly clueless
updated 11.5 years ago • Emma Quinn
Dear Bioconductors, I have been using goseq for GO term and KEGG pathway enrichment analysis for RNAseq data. My question is if it is possible to use goseq for the...these pathways for topological pathway analyses, but I would like to use these pathways for the goseq enrichment approach (where gene length is taking into account). Is there a simple way to combine or integrate these analyses...go…
updated 7.3 years ago • b.nota
I’m trying to run GOSeq with human RNA Seq data that has been processed with Salmon, summarized to gene level with tximport, and DGE run using...DeSeq2.&nbsp; I was reading the vignette for GOSeq and got stuck/confused on the part where you need to know what human genome build you used... It says you need to know this...genome, correct? So then could I just use the avgTX length from the txim…
updated 6.0 years ago • casey.rimland
I installed goseq and when I call: <pre> SO &lt;- supportedOrganisms() Error: could not find function "supportedOrganisms" supportedGenomes...support.bioconductor.org/p/93207/> but following those suggestion did not help. &nbsp; In the goseq Bioconductor site said that the goseq version is 1.26. However when I install it in my mac running R vesrion 3.2.2 I got...have been …
updated 7.0 years ago • colaneri
TA GO:0016616 BGIOSGA013239 BGIOSGA013239-TA GO:0051287 ..................... Goseq code: d &lt;- read.csv("deseq2res.csv", header=T, row.names=1) all_genes &lt;- row.names(d) DE_genes &lt;- all_genes[d$padj&lt;0.05...head(pwf) # calculate GO enrichment using default method GO.WALL &lt;- goseq(…
updated 3.6 years ago • nabiyogesh
I am running GOseq for mouse data using ~800 genes as input and ~8K genes as background lists.&nbsp; Running GOseq I get the same number of enriched
updated 5.8 years ago • sharvari gujja
div class="preformatted">Hi all! I'm trying to install the 'goseq' package but it returns an error. I'm working with the R version 2.11.1 (2010-05-31). The code is: &gt; source("http://www.bioconductor.org...biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). &gt;bioclite("goseq") Using R version 2.11.1, biocinstall version 2.6.10. Installing Biocon…
updated 12.4 years ago • Claudia Calabrese
Hi, The number of genes in a GO geneset determined by goseq is different from what I obtained by querying org.Hs.eg.db. I ran the following: <pre> library(goseq) data(genes) pwf.eg...nullp(genes,"hg19","ensGene") GO.wall.eg=goseq(pwf.eg,"hg19","ensGene", test.cats='GO:BP') head(GO.wall.eg,5)</pre> It shows that GO:0000278 is top candidate and has 922 for numInCat
updated 5.6 years ago • siajunren
I am using goseq to run analysis on my RNA seq data. Previously it had worked for me, but recently, I am encountering an error when trying...I am using goseq to run analysis on my RNA seq data. Previously it had worked for me, but recently, I am encountering an error when trying to load the package. The error reads as ```r &gt; library(goseq) Loading required package: BiasedUrn Loa…
updated 3.1 years ago • avinashi
Hi, &nbsp; I am trying to install goseq package in my R studio 3.2.2 doing the following: <pre> source("https://bioconductor.org/biocLite.R") biocLite("goseq") library...goseq) </pre> After that, I can't use the package because of a problem with&nbsp;geneLenDataBase. I keep receiving the following
updated 8.4 years ago • amyfm
Hi all, I'm using GOseq to analyse RNASeq data. When I run the nullp function to compute PWF, I got this warning message: "Warning message: In pcls
updated 8.8 years ago • Pauly Lin
I am running differential gene (DE) expression analysis using RNA-seq data and I have used GOseq to find enriched Gene Ontology (GO) categories in the DE genes list. I have a couple of questions to ask, and hope someone...can help me: Can I extract the number of genes, and IDs present in each enriched category using GOseq? If not, I suppose it is better to annotate all the genes for GO and fin…
div class="preformatted">Hello, I am trying to use goseq to find enriched GO terms for zebrafish RNA- seq data and am looking for advice on manually providing gene length information...and GO annotation to goseq. My RNA-Seq data is mapped to danRer7 Ensembl gene id's. Unfortunately danRer7 does not appear to be supported by goeqs...mart = zv9) How can I input this GO Data and gene lengt…
<div class="preformatted">Hi all, I have run goseq on RNA-seq data differential expression results, but got a strange p-value distribution: from zero to almost one it is uniformly distributed, but there is a huge enrichment to the value one. See screenshot: https://dl.dropbox.com/u/18352887/Selection_042.png This seems that the distribution underlying the null hypothesis is incorrect? As …
Hi. I work with Prunus persica. Goseq doesn't support it so I perform the GO Analysis 'by hand' like this: &gt;de\_data=read.table("gene\_exp.diff", header=T) &gt;diff...FALSE, sep="\\t") &gt;pwf=nullp(diff\_express, bias.data=length, plot.fit=TRUE) &gt;GO.wall=goseq(pwf, gene2cat=cat\_map) Then I save the GO.wall output, who looks like the one reported on goseq User's…
updated 7.7 years ago • tobal.92
Dear goseq developers: &nbsp; &nbsp; &nbsp;&nbsp;Hello ,my name is Xu,ZhengZheng ,a student of Beijing Institute of Gennomics ,Chinese...Dear goseq developers: &nbsp; &nbsp; &nbsp;&nbsp;Hello ,my name is Xu,ZhengZheng ,a student of Beijing Institute of Gennomics ,Chinese Academics...After I use edgeR to do difference Gene expression ,I happy to&nbsp;known tha…
updated 8.6 years ago • xdzperfect
Using pkg goseq for the first time; I get this error: &gt; pwf = nullp(genes, 'hg19', 'Gene Symbol', bias.data=df$len) Warning message: In pcls(G) : initial...Using pkg goseq for the first time; I get this error: &gt; pwf = nullp(genes, 'hg19', 'Gene Symbol', bias.data=df$len) Warning message: In pcls(G) : initial point very close to some inequality constraints &gt; GO.wall…
updated 8.1 years ago • jdavison
which around 6000 genes are differentially expressed (padjustedvalue &lt; 0.05). Now I want to use goseq in order to study pathways. I am a very amateur R user and I am starting to learn about all this, so I have no idea what I have...do now. By checking this website&nbsp;<http://www.bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf>, I understand that I hav…
updated 8.4 years ago • amyfm
list of about 500 DEG. Now I would like to perform a gene ontology analysis on this dataset with the GOseq package. According to the GOseq user manual, this package requires 2 pieces of information : the differentially expressed
updated 10.1 years ago • amandine.fournier@chu-lyon.fr
Hi, I have a few questions about using goseq on a non-model organism: I have a set of DE-genes identified by DESeq2 called `` genes ``, a vector of gene lengths called `` lengthData...a reference set of genes called `` backM `` which is a list of gene names I am at this point of the goseq manual: <pre> pwf=nullp(genes,"hg19","ensGene")</pre> And my question is how do I refer to…
updated 8.3 years ago • Jon Bråte
nbsp;from TCGA. I got a list of differentially expressed genes by using edgeR. I also performed the goseq analysis and got the results for it. Now, I am trying to extract only those genes that are DE from my list of DE list given...to goseq after the enrichment analysis.&nbsp; I used the following code, but I get an error that is posted below: \#Goseq analysis genes...table\[de.cmn$table…
updated 8.0 years ago • darshinimamindla
dds &lt;- DESeq(ddsMat,betaPrior=TRUE) res &lt;- results(dds) # Extract results library(goseq) genes=as.integer(p.adjust(res$pvalue[res$log2FoldChange!=0], method="BH")&lt;.05) names(genes)=row.names(res[res$log2FoldChange...pwf=nullp(genes,"hg38","ensGene") head(pwf) ``` ![Error message for GO terms analysis with goseq][1] [1]: /media/images/Capture_kzNEGwU.JPG
updated 3.3 years ago • ojong
Hi Matt and Nadia, For almost a year, I was using goseq as a generalized enrichment tool (leveraging the gene length bias correction implemented there, thank you) using my...custom gene sets this way: goseq(myData, genome=NULL, id=NULL, gene2cat = MyVeryOwnGeneCategorization, method="Sampling", repcnt = 100000) After recent update...return an error in any other case). This…
updated 9.1 years ago • Oleg Moskvin
Hello everyone. I recently started using GOSEQ for the analysis of RNA-Seq results from DESeq2. I have around 37K total genes with ~3K differentialy expressed. I am using...span style="line-height:1.6; white-space:pre-wrap">my R version is : __3.1.3__ (2015-03-09), and GOSEQ verison is: </span>__<span style="line-height:1.6; white-space:pre-wrap">goseq\_1.16.2 </span>__ T…
updated 8.9 years ago • Vivek.b
<div class="preformatted">After using edgeR to find differentially expressed genes, I tried to follow the instructions in goseq to correct for length bias. top$table[1:10,1] [1] "ENSG00000138131" "ENSG00000204616" "ENSG00000204876" "ENSG00000118972" "ENSG00000143546...After using edgeR to find differentially expressed genes, I tried to follow the instructions in goseq to correct for le…
updated 13.0 years ago • Naomi Altman
HI ALL, I am working on non model species, and now I want to use GOseq to perform GO and KEGG enrichment analysis. I have found a list of DEGs using DESeq2, FDR &lt;= 0.05, |log2FC| =&gt; 1. However, some...Both of them will set a cut off the number of gene associated in GO term. And I am not sure GOseq can have gene set size option or not. And&nbsp;<span style="line-height:1.6"&…
updated 8.7 years ago • jackipchiho
Hi All, I'm currently working on a differential gene expression analysis and I've used GOSeq to find enriched GO categories, just like what is mentioned here (https://stat.ethz.ch/pipermail/bioconductor/attachments...read.table("ATH_GO_GOSLIM.txt", header=F, sep="\t", fill=T) #read in GO Categories File GO.wall &lt;- goseq(pwf, gene2cat=tairgo[,c(1,6)]) # get ID and GO columns only from tai…
database documentation, the bioconductor mailing list, the &gt; BSgenome documentation, and the goseq documentation, I am still very &gt; confused about whether I can use the assembly 4 package that Herv? &gt; 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.…
I’m currently&nbsp;attempting&nbsp;to perform an&nbsp;analysis&nbsp;using GOseq on the&nbsp;up regulated&nbsp;genes of a RNAseq experiment.&nbsp;The&nbsp;thing is I keep getting a plot as the one I attached
updated 8.5 years ago • dlsoltero
192 results • Page 1 of 4
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