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 <- goseq(pwf, gene2cat=tairgo[,c(1,6)]) # get ID and GO
columns
only from tai…
Order by: Relevance
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.assembly4...that I would presume that it will have more current information than
the
> natively supported (by goseq) Apis release 2.
It's a more recent assembly so I would expect it to be more accurate
(i.e. closer to reality).
&am…
updated 13.6 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
updated 10.1 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…
updated 7.8 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…
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 …
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...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...I would p…
updated 13.6 years ago • Alicia Oshlack
I am trying to perform a GO analysis of differentially expressed genes with GOseq, but I get a very poor fit of pwf by the nullp function.
A bit of context:
- I used bowtie to map the reads onto the transcriptome...I am trying to perform a GO analysis of differentially expressed genes with GOseq, but I get a very poor fit of pwf by the nullp function.
A bit of context:
- I used bowtie t…
updated 18 days ago • f
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…
updated 8.0 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…
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
updated 10.4 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…
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) …
updated 4.6 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
updated 9.4 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> …
updated 8.2 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
updated 4.5 years ago • Lucky
Hej, I am trying to install the Goseq package, but I keep getting this error. I tried downloading the GO.db package, but then I get a new error. See below.
I have...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 fai…
updated 8.1 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
updated 9.1 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…
updated 8.6 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…
updated 11.9 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…
updated 5.3 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…
updated 14.5 years ago • Paolo Sonego
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__
updated 8.6 years ago • jesykamelendez
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)
>...GOr=goseq(pwf,gene2cat=gocats)
Using manually entered categories.
Calculating the p-values...
Error in dWNCHypergeo(num_de_incat
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…
updated 7.3 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…
updated 7.6 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…
updated 14.5 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…
updated 10.1 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
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
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
updated 6.7 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…
updated 13.3 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
updated 19 months 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
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...documentation, the bioconductor mailing list,
the
> >> BSgenome documentation, and the goseq documentation, I am still
very
> >>…
updated 13.6 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…
updated 9.5 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
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) …
updated 7.1 years ago • zhu
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
updated 9.7 years ago • Bohdan Khomtchouk
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
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
updated 7.7 years ago • joelrosa
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
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..…
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 …
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…
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: ...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…
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
updated 9.5 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
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…
updated 3.6 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…
updated 6.1 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
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
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
updated 8.1 years ago • heikki.sarin
Hello,
We are trying to find the root issue of why we are having differing final output results from using the same datasets, parameters, functions, R (4.4.1), RStudio ("2024.04.2+764"), and goseq (1.56.0) package versions. Using the code below, I have tried to replicate the results with the exact same cloned repository on multiple computers and operating systems while checking that all steps a…
updated 14 months ago • Danielle
Hello
I got this error when using supportedGenomes() in goseq package:
<pre>
> library(goseq)
Loading required package: BiasedUrn
Loading required package: geneLenDataBase
> head
updated 8.0 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
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
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.…
updated 9.5 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',…
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 12.8 years ago • Abhishek Pratap
Recent ...
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