<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...<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 express…
Order by: Relevance
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
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
updated 8.2 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…
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
updated 8.7 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* …
updated 17 months 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
updated 3 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
updated 5.5 years ago • Jakub
Diana T. Dugas
<diana.dugas@sparc.usda.gov> wrote:
> Hi, Matthew-
> I am a huge fan of your goseq package. I used it often under an
earlier
> installation of R (2.13.0) and have since upgraded to the latest
version
>...myself in need of updating a lot
of my
> favorite packages. While trying to download and install goseq, from
> source("http://bio…
updated 12.1 years ago • Matthew Young
Hi everyone,
I’m testing for GO categories enrichment using goseq (version 1.32.0) under two different approaches (as described below) and I’m getting different numbers of genes per GO...category.
__\#\#\# Approach 1 \#\#\#__
<pre>
> library(goseq)
> gene.vector = as.integer(assayed.genes%in%de.genes) #19,792 total genes (502 DE genes)
> pwf = nullp(gene.vector, …
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…
updated 7.9 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
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)…
updated 6.1 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
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…
updated 7.8 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
updated 11.6 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
updated 3.0 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"&…
updated 8.7 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
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 …
updated 6.2 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
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, …
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…
updated 3.3 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
updated 8.0 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
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
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
updated 8.2 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
updated 12.6 years ago • annaick.carles
using enrichment results that are contained in data.frames? For example, clusterprofiler vs goseq vs topGO.
Thanks
updated 7.3 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…
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
updated 12.0 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 …
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
updated 7.6 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…
updated 10.5 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
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
updated 9.2 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…
updated 26 days 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
updated 3.4 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
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>",
…
updated 5.8 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
updated 2.2 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 12.4 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 10.9 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
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…
updated 7.0 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
updated 6.0 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 …
#!/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…
updated 6.6 years ago • mictadlo
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
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
updated 8.4 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
…
updated 12.1 years ago • Julie Leonard
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…
updated 8.4 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 11.6 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…
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
updated 8.6 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…
updated 9.1 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
…
updated 7.7 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…
updated 12.0 years ago • Paolo Guarnieri
Hi,
On 02.01.2017, I ran an analysis with DESeq2. I ran a similar analysis recently. I used the same input data for both runs! Please see "raw reads" in the excel file ([https://www.dropbox.com/s/g7fyqvn1chdnesh/deseq2\_bugreport\_23102017.xlsx?dl=0](https://www.dropbox.com/s/g7fyqvn1chdnesh/deseq2_bugreport_23102017.xlsx?dl=0)). Even tough the normalized reads and basemean are same in both runs…
updated 6.5 years ago • Mehmet Ilyas Cosacak
other attached packages:
\[1\] DESeq2\_1.10.0 RcppArmadillo\_0.6.200.2.0 Rcpp\_0.12.1 qvalue\_2.2.0 goseq\_1.22.0 geneLenDataBase\_1.6.0 BiasedUrn\_1.06.1 WGCNA\_1.48 RSQLite\_1.0.0
\[10\] DBI\_0.3.1 fastcluster\_1.1.16
updated 8.4 years ago • julie.green
Recent ...
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This part:
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Thank you Tim, this is a great help in getting me started!
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