Bioconductor Forum

div class="preformatted"> Dear BioC, I have a cutom chip with multiple microbial organisms but I am currently only interested in the results for one of these. At what step in the analysis process is it adviced...to remove the other organisms from analysis. I worry that probes specific to those 'other' organisms may contribute to the background noise. In

Annotation Normalization PROcess Annotation Normalization PROcess

updated 19.6 years ago • Bornman, Daniel M

Community, The organizing committee for BioC2020, to be held in Boston on July 29-31, needs organizers to help in planning the event. Participation involves attending approximately monthly remote meetings plus...of the areas of: * Outreach (developing materials, promotion) * Website * Workshop technical organization * Program development * Sponsorship and funding * Code of Conduct …

conference committee Bioc2020 News

updated 6.2 years ago • shepherl

library(GenomeInfoDb) library(BSgenome.Cfamiliaris.UCSC.canFam3) extractSeqlevelsByGroup(species=organism(Cfamiliaris), style="UCSC", group="auto") Error in extractSeqlevelsByGroup(species = organism(Cfamiliaris), style = "UCSC...for Homo sapiens: <pre> library(BSgenome.Hsapiens.UCSC.hg38) extractSeqlevelsByGroup(species=organism(Hsapiens), style="UCSC", group="auto") [1] "chr1" …

genomeinfodb canis familiaris

updated 10.1 years ago • Robert Castelo

Hello, I am trying to manually download data from the recount3 resource ( https://jhubiostatistics.shinyapps.io/recount3-study-explorer/ ), and I obtain the following error: "ERROR: An error has occurred. Check your logs or contact the app author for clarification" Using a query from R (using an old chunk of code) gives another error: ``` library("recount3") gse = recount3::create_rs…

recount recount3

updated 3.0 years ago • franceschini.gianmarco

pointed me to this forum. My objective is to annotate a table of gene expression data "say for organism A" with information on orthologues from "organism B", as an additional column on a table. I watched tutorials online...to download orthologue genes (IDs, names, etc) from a specific species to my local table containing "organism A". As an example, I have table with expression data from Drosoph…

biomart

updated 7.2 years ago • lm795

of the KEGGgraph package, I end up with the following error: ------ retrieveKGML(pathwayid='00010', organism='cel', destfile="/home/cbio/ludwig/test.txt", method="wget") --17:06:46-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/cel/cel00010.xml...in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD /pub/kegg/xml/organisms/cel ... No such directory …

KEGGgraph KEGGgraph

updated 15.7 years ago • Ludwig Geistlinger

to create a custom `` universe `` for the `` enrichPathway `` function?  I am using a non-model organism and want to use only the human genes that my organism possesses as the background.  In general im not sure how to

reactomepa chipseeker Guangchuang Yu

updated 7.9 years ago • andrew.gehrke

on my RNA-seq gene expression data from Oryza sativa japonica. In order to determine the correct organism code to use in EnrichmentBrowser, I followed the link (https://www.genome.jp/kegg/catalog/org_list.html) in the EnrichmentBrowser...I found two possible codes for Oryza sativa japonica, "osa" and "dosa" I get the same unrecognized organism ID error when I use either of those organism codes …

EnrichmentBrowser Oryza_sativa

updated 4.4 years ago • sjw

30835") clust_r3 <- c("54332") # Comparing clusters > clusterSim(clust_as, clust_r1, ont="BP", organism="human", measure="Resnik", combine="rcmax.avg", drop="NULL") [1] NA > clusterSim(clust_as, clust_r2, ont="BP", organism="human", measure...Resnik", combine="rcmax.avg", drop="NULL") [1] NA > clusterSim(clust_as, clust_r3, ont="BP", organism="human", measure="Resnik"…

GO SemSim GOSemSim GO SemSim GOSemSim

updated 13.4 years ago • Guest User

in the vignette: "How to use GOstas and Category to do hypergeometric testing with unsupported model organisms" by M. Carlson, Oct. 31. 2011, because my organism is a non- model organisms. I have obtained the annotation for my gene sets

Annotation GO Organism GOstats Category Annotation GO Organism GOstats Category

updated 14.0 years ago • Henrik De Fine Licht

Hello, I'm trying to use GOSim with yeast but with no luck. The function "setEvidenceLevel(organism="yeast")" doesn't seem to work. Using the org.Sc.sgd.db library, I obtain a long list of GO terms for "856452" Yet, getGOInfo...GO:0010273`$Evidence [1] "IMP" $`GO:0010273`$Ontology [1] "BP" . . . >setEvidenceLevel(organism="yeast") > getGOInfo("856452") Error in getGOInfo("85645…

GO Yeast GOSim GO Yeast GOSim

updated 8.7 years ago • Guest User

using IE/Firefox. Here's the code: > library(KEGGgraph) > url <- getKGMLurl('04330', organism = "hsa") > url [1] ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml > parseKGML(url) failed to load external...entity "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" Error: 1: failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/or…

Organism hgu133plus2 KEGGgraph Organism hgu133plus2 KEGGgraph

updated 16.2 years ago • Fraser Sim

nbsp;I used some annotation software and Python to get a list of counts for hits to each organism, within each sample.  Imported these counts into R, created a combined data table, and then used DESeq2 for comparing...AKA counts(dds, normalized=TRUE), versus the raw counts per million transcripts (CPM) for these organisms, I noticed something interesting.  For some of the higher…

deseq2 rnaseq rna-seq normalization cpm

updated 9.6 years ago • stwestreich

techniques and RNAseq data. I have time-course RNA seq data from multiple different samples, i.e, organs. What I would like to do is extract patterns that are forming in the data going from time 0 up to the last time point. However...to happen only from time point 0-1 in one sample. Given that I have time point data for multiple organs, I would like to find relationships between the way genes…

machine learning deep learning RNAseq MLSeq

updated 6.9 years ago • A

the problem though, try to get the KEGG pathway ?hsa03010? using >getCategoryIndepKGMLurl(?03010?,organism = ?hsa?) It doesn?t produce a valid html link. It should find ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms...but because 'getKGMLurl' returns the invalid ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 03010. xml?, it then returns ?ftp://ftp…

Pathways Organism SIM KEGGgraph Pathways Organism SIM KEGGgraph

updated 16.0 years ago • Fraser Sim

div class="preformatted">Hi, I have a question regarding setting up a two way anova with two factors: organ (5 levels) and treatment (2 levels). I am not sure quite how to set this up. I understand from the user guide in limma how to set...20,000 probes and I have 30 arrays in my columns for my eset (3 replicates of each treatment and organ). Here is what I was using in my script: trts = c("…

updated 14.2 years ago • Grant R Cramer

<div class="preformatted">Hello all, I've been trying to create the most complete possible compound map for an organism, and KEGGgraph was the best approach until now. Someone already worked with graphs metabolites in R? I have a doubt if the KEGGgraph merging process can miss nodes, that's because, looking at the compounds in each reaction: read.delim(paste("http://rest.kegg.jp/lin…

Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph

updated 13.1 years ago • Ricardo Silva

Loading required package: Rgraphviz Loading required package: grid > url <- getKGMLurl('04330', organism = "hsa") > url [1] "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" > parseKGML(url) failed...to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" Error: 1: failed to load extern…

Organism KEGGgraph Organism KEGGgraph

updated 16.0 years ago • Fraser Sim

Hiya, I have blasted the genes of my non-model organism using the KEGG blastKOALA - so have a list of k numbers associated with my genes. I am using clusterprofiler to run...Hiya, I have blasted the genes of my non-model organism using the KEGG blastKOALA - so have a list of k numbers associated with my genes. I am using clusterprofiler to run enrichment...genes could be mapped, so I tr…

kegg enrichkegg clusterprofiler

updated 7.4 years ago • bekah

bacterial pathogen (Mycobacterium tuberculosis) with a virus (rabies virus) `` is.genome.available(organism = "Mycobacterium tuberculosis", db = "refseq") `` <pre> is.genome.available(organism = "Rabies lyssavirus", db = "refseq") </pre> both...reference sequences using the following code: <pre> Mtb.genome.refseq <- getGenome(db = "refseq", organism = "Mycobacteriu…

Genbank biomartr Genomic sequences

updated 7.5 years ago • peter.durr

Hi all,  Just wondering if  anybody can offer some help. I have searched for this answer but unfortunately have not found any solutions I am currently looking at an aging population of a specific cell type in various organs and am interested in looking for differential isoform usage over time.  I have created a Granges object using the...any solutions I am currently…

dexseq differential isoform usage isoforms summarizeoverlaps granges

updated 7.7 years ago • A

nbsp; The aim of this question I have is as follows: Is there a difference in exon usage in each organ going from p3 up to p60. After this, can I identify exons that are deferentially used across all organs or a subset of organs...sampledataalltimepoints:__ colData(SE)$condition=Sampledataalltimepoints$Time\_point colData(SE)$Organ=Sampledataalltimepoints$Organ colData(SE) SE$condition…

DEXSeq differential exon usage

updated 7.5 years ago • A

``` # Install GEOquery if you haven't already > if (!requireNamespace("GEOquery", quietly = TRUE)) { + if (!requireNamespace("BiocManager", quietly = TRUE)) { + install.packages("BiocManager") + } + BiocManager::install("GEOquery") + } > > library(GEOquery) > > search_GEO_series <- function(keywords, organism, source, sample_type, mo…

HELP

updated 11 months ago • ramya20kumar20

NArefLink.txt.gz is incorrect or the target site is not responding! In addition: Warning messages: 1: Organism Lycopersicon esculentum is not supported by GoldenPath (GP). in: getUCSCUrl(organism) 2: Organism Lycopersicon esculentum...is not supported by GoldenPath (GP). in: getUCSCUrl(organism) [1] "1250 2 2" Error in sort.list(unique.default(x), na.last = TRUE) : 'x' must be atomic for …

Annotation Organism AnnBuilder Annotation Organism AnnBuilder

updated 18.6 years ago • Groot, Philip de

I'm trying to run the gost I get this error: ```rNo results to show Please make sure that the organism is correct or set significant = FALSE ``` I've tried both organisms, as well as setting significant to false, but it's not...why it runs on the website but not in R ? ```r GO_Analysis=gost(query=Result_table_B_ASHR$ID, organism = "oaries", ord…

GO RNASeq

updated 2.7 years ago • Nitro

Error: 'recount3_url' is not a valid supported URL since it's missing the URL/ <organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system. ``` </organism

recount recountWorkflow recount3

updated 3.0 years ago • Max Bone

the genes corresponding to the significant GO terms. I have found previous help for supported model organisms, but is there a way to do this for unsupported organisms? Thanks Krys Kelly

gostats unsupported organisms

updated 10.8 years ago • Krys Kelly

gt; > ABPkgBuilder(baseName="mpedbadm_genbank.txt", + baseMapType="gbNRef", + pkgName="MPEDB", + organism="Mus musculus", + otherSrc=c(UG="mpedbadm_unigene.txt"), + pkgPath="./", + version="0.1", + author=list(authors="Denise Mauldin", maintainer...dmauldin at="" fhcrc.org="">")) Warning message: Built for UCSC is not valid! in: getUCSCBuilt(organism) Error in parseKEGGGenome() : Faild…

Organism Biobase annotate AnnBuilder Organism Biobase annotate AnnBuilder

updated 20.1 years ago • Denise Mauldin

of expression of transcripts, but I have a problem how to use "ballgown". I have 36 dataset: 2 organs, 4 time points for each organ, 2 types of light treatment for each time point of each organ and 2 replicates, 2\*4\*2\*2=32...and 2 organs, 1 time points for each organ, 1 types of light treatment for each time point of each organ and 2 replicates, 2\*1\*1\*2=4

ballgown rnaseq

updated 9.1 years ago • noset2769

resulting in the "Error: 'recount3_url' is not a valid supported URL since it's missing the URL/ <organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.". I installed the most recent...seems to not treat a 302 as a successful response and returns FALSE. Running project_homes(organism = "human", recount3_url = "http://idies.jhu.edu/recount3/d…

recount3

updated 3.0 years ago • Cornwell, Adam

human) #save in a TSV format (the file is saved in txt) write.table(tmpgene,"Z:/tomhait/organisms/human/transcript_names.txt", row.names=FALSE, quote=FALSE) #collect all sequences with upstream flank 3000 bases...lt;- with(sequence, nchar(as.character(transcript_flank))) #writing to a new file in "Z:/tomhait/organisms/human/mart_export_new.txt" #you can change it to "mart_export_new.txt" and it …

biomaRt biomaRt

updated 13.3 years ago • Tom Hait

<div class="preformatted">>From: Jing Huang [mailto:huangji@ohsu.edu] >Sent: Wednesday, September 14, 2011 11:00 AM >To: Tarca, Adi >Subject: question for you on SPIA package >Dear Adi, >I have a new question on SPIA package and have sent it to the mailing list a few days ago. I did not received an answer. I am trying again here by sending you the q…

Pathways Organism SPIA Pathways Organism SPIA

updated 14.2 years ago • Tarca, Adi

There is lots to be done, including sponsorship and funding, outreach, website, workshop technical organization, program development, code of conduct communication and enforcement, and local organization. Please fill out

bioc2022 Conference

updated 4.0 years ago • Levi Waldron

argument but, that function is actually using it.  <pre> Error in enrichGO(gene = genelist, organism = org, ont = ont, pvalueCutoff = pvalueCutoff, : unused argument (organism = org)</pre> How can we fix this? The issue\# is 1408. Thanks

software error

updated 9.8 years ago • alper.kucukural

Hi! I am trying to get the promoter sequences of a less well known organism and I am using a simple script I have used many times for model organisms. I am using a GFF file downloaded from NCBI...and I have successfully made the `txdb` object But since I don't have a BSgenome for this organism, the vignette states that I can use a `FaFile` instead, but here is where I am having trouble with `…

Rsamtools GenomicFeatures

updated 3.8 years ago • rbenel

OK Prepare the 'metadata' data frame ... Error in GenomeInfoDb:::lookup_tax_id_by_organism(organism) : Oryza indica: unknown organism. Please use 'loadTaxonomyDb()' to see viable genus/species and taxonomy IDs. ``` How can I...run clusterprofiler package for GO term analysis. Also `GenomeInfoDb:::lookup_tax_id_by_organism(organism)` does not work and lacks manual for reference

GenomeInfoDb OrganismDbi biomaRt

updated 5.1 years ago • rohitsatyam102

trying to run is getting the enrichment results by Over-Representation Analysis with ClusterProfiler. ``` organism = "org.Hs.eg.db" #BiocManager::install(organism, character.only = TRUE) library(organism, character.only = TRUE) # reading...gene = genes, universe = names(gene_list), OrgDb = organism, keyType = 'ENSEMBL', …

enrichplot clusterProfiler org.Hs.eg.db

updated 3.7 years ago • beslinail

I do not know how to install the end product. I also do not know how to interpret the warning message. Hoping for some insight as to where to go from here. Thanks ``` library(AnnotationForge) # https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=32201\ org<-makeOrgPackageFromNCBI(version = "0.1",author ="MT",maintainer = "netname@aol.com",outputDir = "C:\\Users\\mat14\\One…

AnnotationForge makeOrgPackageFromNCBI

updated 2.1 years ago • mat149

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

clusterProfiler ggpubr

updated 20 months ago • BCS12

I am trying to make a TxDb package from a gff3 file for an organism not available from UNSC. I can successfully make the TxDb like so: <pre> library(GenomicFeatures) txdb <- makeTxDbFromGFF...file="file.gff3", dataSource="Organism Genome Project", organism="My organisim")</pre>   However when I to make the package…

genomicfeatures txdb

updated 9.0 years ago • gtho123

there are 5586 genes with GO annotation. In WebGestalR: ```r enrichD_BP <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Biological_Process_noRedundant") geneSet_BP <- enrichD_BP$geneSet...length(unique(geneSet_BP$gene))#9011 enrichD_CC <- loadGeneSet(organism = "btaurus",enrichDatabase = "geneontology_Cellular_Component_noRedundant") geneSet_CC &am…

clusterProfiler WebGestalR

updated 3.4 years ago • pengmin.wang.1

I have a list of uniprot protein IDs and NCBI taxonomy IDs for the organism that contains the protein. For each combination, I want the DNA sequence that codes for the protein (CDS) in the organism

ensembldb biodbUniprot

updated 2.9 years ago • Peter

pub/Chaix2008/CEL/supplCELdata.zip With BioConductor Is there a way we can find: 1. Which organism they come from? 2. Which organism's tissue they come from? 3. What are the probe names/gene name involved? I looked at "affy

Organism probe Organism probe

updated 17.2 years ago • Gundala Viswanath

Dear community members, I am currently working with the microbiome analysis of a plant using the RNASeq data. I have 3 replication with 2 treatment data. I have normalized count data of each microbe in the above data sets. I was wondering if I could take the count data and use edgeR to calculate the foldchange of the organism? Say, I may get staphylococcus aureus is 3 log2FC upregulated i…

edger

updated 5.3 years ago • megha.hs28

in a BioC mailing list and fired up a following; testcount<-easyRNASeq(filesDirectory=getwd(), organism="Hsapiens", chr.sizes="auto", readLength=100L, annotationMethod="gtf", annotationFile="Ensemble.gtf", count="exons", outputFormat...arguments... Fetching annotations... Read 2280612 records Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = "auto", : The…

Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2

updated 12.2 years ago • Aki Hoji

but worth fixing. First warning that is shown: Built for UCSC is not valid! in: getUCSCBuilt(organism) The offending function is the following. > get('getUCSCBuilt', envir=environment(ABPkgBuilder)) function (organism...url <- getSrcUrl(src = "GP", organism = organism) built <- NA if (is.na(built) || is.null(built) || built == "") { warning("Built for UC…

GO Organism reposTools AnnBuilder Resourcerer GO Organism reposTools AnnBuilder

updated 20.1 years ago • Francois Pepin

status, group=strand, data=res, auto.key=TRUE)) #But then, if I want to retrieve the EC numbers and organism info for the viral proteins on Uniprot, this should work: # (I did it first through http://www.ebi.ac.uk/uniprot/biomart...I use checkFilters = FALSE # Using the website app, I do get information back. # If I check only the "organism" attribute, then I do get some information. virus2 &…

Organism biomaRt Organism biomaRt

updated 16.3 years ago • Leonardo Collado Torres

eset), + pvalueCutoff=0.05) > temp <- hyperGTest(temp.params) Error: 'ORGANISM:Drosophila melanogaster' is not a supported. organism must be one of: ORGANISM:Homo sapiens, ORGANISM:Mus musculus

GO Organism drosophila2 GO Organism drosophila2

updated 16.6 years ago • Paolo Innocenti

the pathway information that related to differentially expressed the genes. However, some organisms such as Drosophila are not included in the package. I downloaded the data but not sure how to incorporate the data...dmeSPIA.RData") Here is the R scripts for predicting the pathways: res=spia(de=CH,all=CH1,organism="dme",nB=2000,plots=F,beta=NULL,combin e="fisher",verbose=F) Many THANKS Jing …

PROcess SPIA PROcess SPIA

updated 14.2 years ago • Jing Huang

Hello, I am exploring the new AnnotationHub package and I find it fantastic. Thank you for all the effort, and also for the nice tutorials on coursera and youtube. I do not understand how much AnnotationHub will replace existing packages such as AnnotationDbi or the organism packages. For example I wonder if there is a way to convert an Entrez Id to convert gene Entrez to symbols and other IDs …

conversion symbol entrez

updated 10.2 years ago • dalloliogm

R ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'BSgenome(organism = "Oryza sativa", ': 参数没有用(nmask_per_seq = .nmask_per_seq, masks_pkgname = pkgname, masks_dirpath = extdata_dirpath) ** help...onLoad failed in loadNamespace() for 'BSgenome.Osativa.MSU.MSU7', details: call: BSgenome(organism = "Oryza sativa", species = "Rice", provider = "MSU", e…

Oryza_sativa AnnotationDbi

updated 4.7 years ago • 耀宇

Microsoft PowerApps has transformed the way organizations build and use applications. By offering a low-code platform, it empowers businesses to create tailored apps...must continuously maintain, optimize, and scale their PowerApps solutions. This is why more organizations are investing in ongoing PowerApps Support Services. From troubleshooting issues and improving performance

chipenrich

updated 11 weeks ago • john

will be helpful. The R script as follows, ``` proteome <- biomartr::getProteome(db = "refseq", organism = "Arabidopsis thaliana") annotation <- biomartr::getGFF(db = "refseq", organism = "Arabidopsis thaliana") # retrieve longest

FunctionalAnnotation StatisticalMethod

updated 4.5 years ago • Aneesha

head(dds_selected) library(KEGGREST) library(limma) enrichKEGG(gene = dds_selected, organism = "hsa", pvalueCutoff = 0.05, use_internal_data = TRUE) enrichKEGG( gene = dds_selected, organism = "hsa", keyType = "kegg", pvalueCutoff

KEGGREST enrichment KEGG

updated 3.4 years ago • Soha F

a conceptual question. I have the aim of testing the hypothesis that genomic windows within an organisms genome might have higher read mapping abundances than the same region for a different organism. I am wondering

edger differential expression

updated 5.7 years ago • hollandademello

encouraged. Workshops can vary in length, but most will be one full day in duration. Workshop organizers and attendees must register for their workshop and are permitted to join the main BIRD conference. Requirements...The names, affiliations, postal address, phone and fax numbers, and e-mail addresses of the workshop organizers (It is expected that organizers will be recognized experts in the re…

PROcess PROcess

updated 18.4 years ago • Prof. Roland Wagner

using clusterprofiler and the gseKEGG function. I am working on C. perfringens which is a KEGG organism as far as I know. I've put my code below, but basically when I try run the command I hit an error where when it tries to access...My gene list is in Entrez ID format. ```r gsea_results <- gseKEGG( geneList = geneList, organism = "cpf", # KEGG organism code for Clostridium perf…

clusterProfiler KEGG

updated 9 months ago • Jessica

with lfcShrink (apeglm). I apply the analysis between healthy and diseased samples for multiple organs. However the healthy samples for almost every organ are about 1-15% of the diseased samples (eg. 44 healthy vs 525 diseased...130 vs 903 or even 3 vs 309!). I do get results for almost every organ studied, but I am skeptical on the actual statistical significance of said results and the amoun…

deseq2 cancer

updated 6.0 years ago • thanos5541

hi everybody, I'm trying something seemingly simple but it segfaults and I wonder it this might be a bug? I run: " library(GOSim) library(org.Hs.eg.db) library(org.Mm.eg.db) library(GO.db) setEvidenceLevel(evidences = "all", organism=org.Hs.egORGANISM, gomap=org.Hs.egGO) calc.diffusion.kernel(method="diffKernelLLE", m=5, normalization.method="sqrt", DIR="/tmp") " and it fails…

go.db software error bug

updated 10.6 years ago • lejeczek

message stating that Error in download.KEGG.Module(species) : _  'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org\_list.html'..._ Even I tried to to use the example from vignette, and...nbsp;             xx <- enrichMKEGG(de, organism = 'hs…

clusterprofiler

updated 7.4 years ago • bright602