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',…
Order by: Date
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 6.7 years ago • heikki.sarin
Hi all,
I'm using PANTHER.db to run some enrichment analysis and am trying to use the function pthOrganisms to restrict the database to mouse. More specifically, the code is:
pthOrganisms(PANTHER.db) = "MOUSE"
However, I obtained the following error:
Error: could not find function "pthOrganisms"
The package installs just fine and the library loads correctly. Page 3 of the…
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 6.8 years ago • david.rinker
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.  ...relevant threads below), but I'm not sure if anyone ha…
updated 6.8 years ago • krc3004
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
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 installed goseq and when I call:
<pre>
SO <- supportedOrganisms()
Error: could not find function "supportedOrganisms"
supportedGenomes...support.bioconductor.org/p/93207/>
but following those suggestion did not help.
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 7.1 years ago • colaneri
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 7.2 years ago • jesykamelendez
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…
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 7.2 years ago • tootiki
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…
using enrichment results that are contained in data.frames? For example, clusterprofiler vs goseq vs topGO.
Thanks
updated 7.3 years ago • fizer
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…
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
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 7.6 years ago • webquelzinhablue
Dear goseq developers and all,
Following the question here
https://support.bioconductor.org/p/60759
The code in Goseq manual says
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
Hi.
I work with Prunus persica. Goseq doesn't support it so I perform the GO Analysis 'by hand' like this:
>de\_data=read.table("gene\_exp.diff", header=T)
>diff...FALSE, sep="\\t")
>pwf=nullp(diff\_express, bias.data=length, plot.fit=TRUE)
>GO.wall=goseq(pwf, gene2cat=cat\_map)
Then I save the GO.wall output, who looks like the one reported on goseq User's…
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
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 …
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
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 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..…
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
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 8.0 years ago • Mehmet Ilyas Cosacak
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 8.1 years ago • mrodrigues.fernanda
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.
I used the following code, but I get an error that is posted below:
\#Goseq analysis
genes...table\[de.cmn$table…
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 8.1 years ago • mrodrigues.fernanda
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">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…
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 8.1 years ago • mrodrigues.fernanda
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
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
Using pkg goseq for the first time; I get this error:
> pwf = nullp(genes, 'hg19', 'Gene Symbol', bias.data=df$len)
Warning message:
In pcls(G) : initial...Using pkg goseq for the first time; I get this error:
> pwf = nullp(genes, 'hg19', 'Gene Symbol', bias.data=df$len)
Warning message:
In pcls(G) : initial point very close to some inequality constraints
> GO.wall…
updated 8.2 years ago • jdavison
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 8.3 years ago • Bohdan Khomtchouk
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 <- nullp(gene.vector, "hg19", "geneSymbol", bias.data = lengthhg19)
GO.wall <- 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 8.3 years ago • b.nota
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 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,
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 8.4 years ago • Jon Bråte
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
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 8.5 years ago • julie.green
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
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
which around 6000 genes are differentially expressed (padjustedvalue < 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 <http://www.bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf>, I understand that I hav…
Hi,
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 geneLenDataBase. I keep receiving the following
updated 8.5 years ago • amyfm
RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund"))
I could
updated 8.6 years ago • anna.dolnik
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
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 8.7 years ago • dlsoltero
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 …
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 8.7 years ago • xyliu00
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
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
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
Dear goseq developers：
Hello ,my name is Xu,ZhengZheng ,a student of Beijing Institute of Gennomics ,Chinese...Dear goseq developers：
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 known tha…
updated 8.8 years ago • xdzperfect
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 <= 0.05, |log2FC| => 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 <span style="line-height:1.6"&…
updated 8.8 years ago • jackipchiho
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
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 8.9 years ago • Pauly Lin
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 9.0 years ago • idomtamir
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
Recent ...
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Many thanks and it also resolved the same issue for me!
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I tried egsea.ma and got this error:
gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
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Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
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sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
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