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 …
Order by: Date
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…
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 9.2 years ago • suzy.stiegelmeyer@syngenta.com
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
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>
> library(goseq)
> library…
updated 9.3 years ago • M.Gierlinski
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
> GO.wall = goseq(pwf, "sacCer3", "ensGene")
Fetching GO annotations...
Error in toTable(get(paste(orgstring, "GO2ALLEGS", sep = ""))) :
error in evalua…
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 9.3 years ago • Oleg Moskvin
Previously, I invoked runValue (strand (GRangesList)) in order to extract strand information for a GRangesList object. However, upon updating to R 3.1.2 and Bioconductor 3.0, this code no longer works:
> refSeqDb = suppressWarnings (makeTranscriptDbFromUCSC (
"hg19",
tablename = "refGene"))
> h…
updated 9.5 years ago • Robert K. Bradley
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
genes belong to specific gene ontologies to infer different functions between my groups. I used goseq package to make GO analysis and finally obtained the list of significatively over-represented GO with their associated
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
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…
<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…
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…
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…
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…
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
<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…
<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 10.5 years ago • 刘鹏飞
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
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 10.6 years ago • 刘鹏飞
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->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…
updated 11.0 years ago • Xulong Wang
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->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…
updated 11.0 years ago • Guest User
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 11.0 years ago • Emanuela
<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
<div class="preformatted">
Hi All,
I aligned my RNA-seq data using ensemble igenome for cattle and used
edgeR for DE identification. I wanted to use goseq but I got this
error:
>pwf=nullp(genes,"bosTau4","ensGene")
Loading bosTau4 length data...
Error in qr.R(qrx) :
could not find symbol...RNA-seq data using ensemble igenome for cattle and used
edgeR for DE identification. I want…
Re: displaying the image with EBImage (Nima Ahmadian)
21. Re: Negative parameter error when using goseq (Nadia Davidson)
22. Re: anova like test in edgeR (Gordon K Smyth)
23. Re: Subsampling of BAM/SAM alignments (Martin Morgan)
24
updated 11.2 years ago • Matthew Thornton
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
<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 …
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
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
<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 …
updated 11.5 years ago • Joachim Jacob
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
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 < 0.05) into goseq?
It
sounds obvious, but I'm not sure.
Also I have some questions regarding the g…
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
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,
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
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
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…
updated 11.7 years ago • Ravi Karra
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 11.9 years ago • steve Shen
<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
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 12.1 years ago • Julie Leonard
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 12.1 years ago • Julie Leonard
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
<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
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…
updated 12.2 years ago • Matthew Young
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
div class="preformatted">Page 3 of the goseq documentation states
"In order to link GO categories to genes, goseq uses the organism
packages from Bioconductor.
These...string identifying
the genome and <id> is a short string identifying the gene identi_er.
Currently, goseq will
automatically retrieve the mapping between GO categories and genes
from the relevant package
(as long as it is…
updated 12.2 years ago • Corby, Vanessa
Alpesh Querer <alpeshq@gmail.com>
> > To: bioconductor@r-project.org
> > Subject: [BioC] Goseq plot
> > Message-ID:
> > <cao0xdqpci- dntu+yckafuf6h5wdjofj954ot+ktrto_ngu="xFA@mail.gmail.com">
> > Content-Type...text/plain
> >
> > Hi Goseq ers,
> >
> > I followe…
updated 12.2 years ago • Alpesh Querer
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.…
updated 12.2 years ago • Alicia Oshlack
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...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…
updated 12.2 years ago • Hervé Pagès
gt; To: bioconductor <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] GOSeq error
> Message-ID:
> <1328880137.28802.YahooMailNeo at web86706.mail.ird.yahoo.com>
> Content-Type: text...plain; charset="iso-8859-1"
>
> Hello List
>
> I'm using GOSeq to examine the biology behind genes found to be
regulated in a
&a…
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) < lower_bound) fv = fv - min(fv) + lower_bound :
? missing value
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 12.5 years ago • Christopher T Gregg
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:
> source("http://www.bioconductor.org...biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
>bioclite("goseq")
Using R version 2.11.1, biocinstall version 2.6.10.
Installing Biocon…
<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…
text/plain
>
> Hi All,
>
> Using goSeq to analyze two gene lists - up regulated and down
regulated
> genes generated with edgeR, the up regulated list seems...gt; 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 man…
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…
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 12.7 years ago • annaick.carles
Recent ...
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Comment: all variables in design formula must be columns in colData (Deseq2) error
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thank you!
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coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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robersy
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Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
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Hi Michael, thanks a lot for your prompt reply!
Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
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•
0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
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