<div class="preformatted">I am trying to integrate several diverse affy datasets
from the GEO database all from the same organism
same chip design (~500 samples).
I'm interested in obtaining absolute expression values
and have created a robust target...I am trying to integrate several diverse affy datasets
from the GEO database all from the same organism
same chip design (~500 samples).
I…
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gt;> differential expression analysis comparing the cell samples
with
the
>>>>> organ samples, you need to normalize
>>>>> all the samples together.
>>>>>
>>>>> --Naomi
>>>>>
>>...…
updated 18.2 years ago • Bogdan Tanasa
Dear all,
I am slightly confused and I d like your help.
I want to use the [Chipseeker](https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html) package of Bioconductor.
It is required for using some functions to have an annotation DB file, as you see in the picture. The problem is that the genome is new, and the annotations are not published yet.…
updated 2.9 years ago • L
Hello everyone,
I need to download whole protein-protein interaction network of Mus musculus. I downloaded from STRING but the file is too big to manipulate (about 12 million lines). I need to delete some interactions with low confidence score but I cannot open this file with Matlab, R, Python or Excel.
I really need to find this network. Has anyone ever download such a network with a pac…
updated 7.7 years ago • hkarakurt
Hello,
Does anyone know of a way to get a list of ENSEMBL gene identifiers for all known tRNA encoding genes for a given species?
At the moment, I am interested in generating such lists for human and mouse.
For other types of genes (rRNAs, snoRNAs, etc.) I am able to use biomaRt to find all such genes, for example:
library(biomaRt) ensembl_mart = useMart(biomart="ensembl") biomart = useDa…
updated 10.7 years ago • Keith Hughitt
of pathways returned by keggPathwayGraphs.
```r
kegg_mmu <- ROntoTools::keggPathwayGraphs(
organism = "mmu", updateCache = TRUE
)
kpn <- ROntoTools::keggPathwayNames(
organism = "mmu", updateCache = TRUE
)
> length(kegg_mmu)
[1] 222
updated 3.4 years ago • abf
gt; >> > tmpXML <- "testKGML1.xml"
> >> > retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML,
> >> > method="wget")
> >> --2010-09-21 12:23:04--
> >>
> >>
> ftp://ftp.genome.jp/pub/kegg...kgml/non-
metabolic/organisms/mmu/mmu05213.xm…
Hi all,
I'm using clusterProfiler to check a list of genes for KEGG pathway enrichment.
While that list of genes did not show any significant enrichment (as was expected), I was still curious which pathways they mapped to.
To figure this out, I set `pvalueCutoff=1` and `qvalueCutoff=1` assuming that the result should then show me all pathways to which genes map. However, the analysis onl…
updated 3.6 years ago • michaelR
project %in% c(projects) & project_type == "data_sources"
)
proj_info
project organism file_source project_home project_type n_samples
33 SRP013565 human sra data_sources/sra data_sources 2212
updated 4.2 years ago • António Miguel de Jesus Domingues
WebGestaltR")
outputDirectory <- getwd()
enrichResult <- WebGestaltR(enrichMethod="ORA",organism="dmelanogaster", enrichDatabase="pathway_KEGG",interestGeneFile=geneFile,interestGeneType="genesymbol", isOutput
updated 3.9 years ago • Chise
Z disc
5 GO:0042805 actinin binding
6 GO:0045214 sarcomere organization
head(sorted_genes)
[1] "130662847" "130662842" "130662836" "130662822" "130662814" "130662313
updated 23 months ago • nromerov
precompiled
binary
from CRAN), and Bioconductor. I have the Affymetrix-provided cdf file
for my
organism (Fusarium graminearum). I have not had much luck finding the
source
package installation files that the makecdfenv
updated 19.7 years ago • Heather Erika Hallen
<div class="preformatted">Hello,
I am performing GO term enrichment analysis in my organism of interest
(bos taurus) using the org.Bt.eg.db and GO.db package. However, since
the GO.db package uses the "lite" version...div class="preformatted">Hello,
I am performing GO term enrichment analysis in my organism of interest
(bos taurus) using the org.Bt.eg.db and GO.db package. However, sin…
updated 11.4 years ago • Eric Fournier
from well-controlled experiments
are 0.4 for human data, 0.1 for data on genetically identical model
organisms or 0.01 for technical replicates."
The species that I am studying is not Homo sapiens and despite it is
the same species
updated 12.5 years ago • Guest User
Hi,
I am in the process of designing an RNA-seq experiment with a non-model organism. I would like to have 3 treatments/groups, and analyze my data with a gene coexpression network analysis like WGCNA
updated 6.6 years ago • Mau
the clusterProfiler version is 3.0.4,here are the errors i met when i use this pakage in Rstudio. Thank you for your answers and this will help many people who use this pakage.
1.Error about use\_internal\_data=FALSE
library(clusterProfiler)
library("DOSE")
data(geneList)
gene <- names(geneList)\[abs(geneList) > 2\]
head(gene)
\#\[1\] "4312" &…
updated 9.5 years ago • happylittlepig
will be mailed next week. You must
register (at least give the number of people from your
organization who would attend). To register, reply directly
to me and please add the [BioCBUG] tag to your subject
heading.
Please
updated 22.2 years ago • Vincent J. Carey, Jr.
in User's guide deal with human, and I couldn't find
where and how I can change to different organism, or define the
chromosome properties.
Thanks,
Lyudmila
Dr. Lyudmila Mikhaylova
Research Associate
Tufts University
gt; # Supporting package: GenomicFeatures
#> # Data source: UCSC
#> # Genome: hg19
#> # Organism: Homo sapiens
#> # Taxonomy ID: 9606
#> # UCSC Table: knownGene
#> # Resource URL: http://genome.ucsc.edu/
#> # Type of Gene ID...gt; # Supporting package: GenomicFeatures
#> # Data source: UCSC
#> # Genome: hg38
#> # Orga…
updated 3.0 years ago • Lluís Revilla Sancho
at <a href="http://www.bioconductor.org/packages/release/bioc/vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.pdf" target="_blank">http://www.bioconductor.org/packages/release/bioc/vignettes/GenomeInfoDb...inst/doc/Accept-organism-for-GenomeInfoDb.pdf</a>
'select()' returned 1:1 mapping between keys and columns
Error: logical subscript contains
updated 8.8 years ago • Leonardo Collado Torres
the kegg errors) until this
error:
library(Resourcerer)
resourcerer2BioC("Agilent_Human1Av2.zip", organism="human",
destDir=file.path(.path.package("Resourcerer"), "temp"),
pkgName=("AgilentHuman1Av2"), srcUrls=getSrcUrl("all","Homo
updated 20.6 years ago • Morten
Dear all,
I am analyzing microarray data for Affymetrix yeast2 chip, I know that
there are two organisms pombe and cerevisiae on this chip. I need to
filter out pombe probesets. There are total 10928 probesets on yeast2
updated 18.1 years ago • Guiyuan Lei
chr [1:8] "333883" "11801" "667410" "16186" ...</pre>
<pre>
gs = gosummaries(gl, organism = "mmusculus")
Error in data.frame(Query = NA, gpr) :
arguments imply differing number of rows: 1, 0</pre>
I am wondering if ‘GOsummaries
updated 10.6 years ago • alakatos
makeLinkedTxome(indexDir=indexDir,
source="Ensembl",
organism="Homo sapiens",
release="98",
genome="GRCh38",
fasta=fastaPath,
gtf=gtfPath,
write=FALSE)
```
an error occurs:
```
Error: lexical error
releases will
only contain 'db' packages. Most db packages now contain Ensembl
accessions,
New 'organism' packages are available for several model organisms:
human,
org.Hs.eg.db; mouse, org.Mm.eg.db; rat, org.Rn.eg.db...fly, org.Dm.eg.db; malaria, org.Pf.plasmo.db. Many of
these packages contain additional organism-specific annotations, e.g.,
flybase (Drosophila) or Jackson Laboratories (mouse…
updated 17.7 years ago • Martin Morgan
rm(list=ls())
ensembl_mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org")
organism <- useDataset(dataset = "hsapiens_gene_ensembl", mart = ensembl_mart)
txdb <- makeTxDbFromBiomart(dataset = "hsapiens_gene_ensembl...filters = "biotype",
values = c("protein_coding"),
mart = organism)
genes[genes$ensembl_transcript…
updated 7.9 years ago • hihi.joshi
that addresses to a certain degree this frustration.
Zotero
A research tool that helps you gather, organize, and analyze sources.
www.zotero.org
Labmeeting
Organize, search, and store your paper collection and lab protocols
updated 16.8 years ago • Anderson Brown
Gene ID (NCBI) and then use SQLForge to create a custom
annotation package which would use an organism .db0 package.
HTH,
J.
Hooiveld, Guido wrote:
> Dear list,
>
> Question for the more knowledgable people:
> A collegue...far as we are able to
> understand the packages use the info available in the corresponding
> organism .db0 packages. However, it is…
updated 16.2 years ago • James F. Reid
run an example query (runs instantaneously, pretty much)
gplInfo = dbGetQuery(con,'select gpl,title,organism,manufacturer from
gpl')
# example of results
gplInfo[82:86,]
gpl title
organism manufacturer
82 GPL92 Affymetrix GeneChip
updated 15.8 years ago • Sean Davis
names
In addition: Warning message:
In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, :
I'm missinoblem og column(s): 'entrezid'. The corresponding database column(s) will be empty! 
s example, the background genes have 7164.
kk <- enrichKEGG(gene = gene,
organism = 'hsa',
pvalueCutoff = 0.05)
head(kk)
<code>...</code>
<code>## BgRatio pvalue p.adjust qvalue
## hsa04110 124/7164 1.706341e-07 2.951969e...rgb(248, 248, 248)"> <- e…
updated 9.0 years ago • nature.hunger
<div class="preformatted">Dear Dadi,
I will need a little more information from you. In addition, it's best
if you post such emails to the bioconductor mailing list (which I've
Cced, so please "answer to all" when you reply.). See there for
subscribing: http://www.bioconductor.org/help/mailing-list/. What I
need to know from you first is what is described in that page:
http://www.bioconduc…
updated 13.3 years ago • delhomme@embl.de
baseName=myBase, srcUrls=mySrcUrls,
baseMapType=myBaseType,
pkgName="myPkg", pkgPath="C:\tmp", organism="human", makeXML=F)
[1] "It may take me a while to process the data. Be patient!"
Error in url(sourceURLs[["GO"]], open = "r") :
Object "sourceURLs
updated 21.3 years ago • Elisabetta Manduchi
<div class="preformatted">Hi,
Suppose this situation:
There is a structure in a cell. This one is composed by five
proteins. All that is essential. But, in that organism only three are
known.
If I have the expression for all genes, is it possible to cluster
all expression in relation to...is a structure in a cell. This one is composed by five
proteins. All that is essential. But…
800,
pvalueCutoff = 0.05,
verbose = TRUE,
OrgDb = organism,
pAdjustMethod = "none")
#Error in abs(stats) : non-numeric argument to mathematical function
updated 5.0 years ago • María
has 25556 mapped keys (of 48803 keys)
DB schema: HUMANCHIP_DB
DB schema version: 2.1
Organism: Homo sapiens
</div
up1000seqs <- getSeq(genome, up1000)
background <- makeBackground(MotifDb.Hsap.PFM, organism = Hsapiens, bg.seq = up1000seqs, type="logn", bg.len = 1000)
I get the following error:
<pre>
Error in (acgt.count/sum(acgt.count
107276640", "9266093", "9270198", "4346096", "4343818"). kk <- enrichKEGG(gene=entr, organism="osa", minGSSize=5, pvalueCutoff=0.05, pAdjustMethod = "BH")`.
The result is data.frame(kk):
ID Description GeneRatio BgRatio
updated 6.9 years ago • zhang.jianhai
I am doing differential expression on a fairly large RNA-Seq dataset, where multiple organs are obtained from the same mice. I would like to model the effects of individual mice using limma's random effects via
updated 8.3 years ago • maltethodberg
<div class="preformatted">This two day course is described in a preliminary way at
https://github.com/vjcitn/bosBiocTrain . Registration form can also
be acquired at that site.
Academic fee: $450; Commercial fee: $750. All proceeds are used
to defray expenses of room rental and to fund the activities of the
Bioconductor Foundation of N.A. Inc., a 501(c)3 charitable
organization.
Course…
updated 12.3 years ago • Vincent J. Carey, Jr.
<div class="preformatted">Hello all,
Thankyou for your suggestions yesterday (re: getting started), they
were
extremely helpful. Now I have a more specific question about the limma
User's guide. In section 8.2 on the 2-sample w/reference method, the
plot commands reference an object "genelist" that points nowhere for
me.
I have to delet the item to get the command to work, and this causes
r…
__ I would like to identify differentially expressed gene orthologs across multiple related organisms. I predicted a set of single copy orthologs from transcriptome de novo assemblies and quantified expression
updated 7.5 years ago • al-ash
Hi,
I?m using the gosummaries() function on an eBayes() MArrayLM object. All is well down to lfc = log2(1.35), using the following expression:
GOsum1 <- gosummaries(efit, p.value = 0.05, lfc = log2(1.35), go\_branches = c("BP"), min\_set\_size = 5, max\_set\_size = 1000, adjust.method = "fdr", exp = NULL, annotation = NULL, components = c(1), max\_signif = 40, show\_genes = FALSE, n\_gen…
updated 7.9 years ago • jan.soderman
r
midt <- MIDTList("Transcriptomics" = mad_filtered_reads,"Amino Acids"= amac, "Organic Acids" = orgac, "Microbiome" = mic, colData = storage)
## Output:
##An object of class MIDTList.
##Tables:
## features individuals miss.indv...Transcriptomics 10000 24 4
##Amino Acids 22 24 4
##Organic Acids 3 16 …
updated 4.5 years ago • Lisa
use.
>
> Use the GenomicFeatures package to build a gene annotation database
> for your organism. By getting a bit more intimate with that package
> (good place to start is by reading its vignette, along with that...to get the sequence
from
> your genome using the appropriate BSgenome.* package for your
> organism. The Biostrings::getSeq function could do…
updated 14.1 years ago • Yating Cheng
268379", "268859", "215999", "22295", "17289")
compareCluster(geneCluster=l, fun="enrichKEGG", organism="mmu", pvalueCutoff=0.05, pAdjustMethod="BH")
And I get:
The following `from` values were not present in `x`: .id
Error in `$<-.data.frame...replacement has 0 rows, data has 31
Using:
<pre>
compareCluster(geneCluster=l, fun="enrichKEGG", organism="hsa", p…
updated 7.0 years ago • unamourdeswann
ret)
199100
> entrez_search(db="sra",
term="\"homo sapiens\"[Organism] \"rna seq\"[Strategy] transcriptomic[Source] illumina[Platform]",
retmax=0)
Entrez search result with 238656 hits (object...contains 0 IDs and no web_history object)
Search term (as translated): "Homo sapiens"[Organism] AND "rna seq"[Strategy] A ...
…
updated 7.6 years ago • langmea
Postdoctoral Fellow will:
* Be part of the Computational Sciences group in the Discovery Sciences organization within Janssen Pharma R&D.
* Be part of the Population Analytics team which is a new, dynamic initiative focused...and outside Janssen.
* Perform and publish high-quality research relevant to the mission of the organization.
* Effectively communicate data and results to …
updated 9.4 years ago • Johnson.Johnson.Careers
the "KEGG Orthology to Genes mapping" as the `universe`?
enr_results <- enrichKEGG(DEG$KEGG, organism='ko', universe = Transcriptome$KEGG, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05, minGSSize = 5)
Here are what
updated 2.8 years ago • ruiqi.li
microarrays and
would
like to do some pathway analysis. KEGG has quite a number of pathways
for
this organism (see
http://www.genome.jp/kegg-
bin/show_organism?menu_type=pathway_maps&org=cdf),
but when I tried to access them
instead
of org.Mm.egCHRLOC which makes code that uses this annotation having
to
know about the organism - why does it have to be be hard coded?
Ideally
I'd like to be able to do the following:
> library(org.Mm.eg.db)
> myGenomeAnnotationFunction
updated 15.1 years ago • arne.mueller@novartis.com
Stanford", "Ross Hardison, PennState", "Michael
Snyder, Stanford", "Ross Hardison, PennState" ), organism = structure(c(3L,
3L, 3L, 3L), .Label = c("Drosophila melanogaster", "Homo sapiens", "Mus
musculus"), class = "factor"), assembly = c("mm9", "mm9...class =
"data.frame", .Names = c("Factor", "assay", "Tissue", "Replicate", "lab",
"organism", "assembly", "bamReads", "Peaks", "lab_short", …
updated 9.6 years ago • liz.ingsimmons
profiles and associated evolutionary distances to
understand biological function and network organization. Applicants
should have extensive training in bioinformatics/computational
biology. Excellent programming
library(GenomicFeatures)
txdb <- makeTxDbFromGFF("./m.tub1.gff3",circ\_seqs=character(), organism="Mycobacterium tuberculosis")
peakAnno <- annotatePeak(peak1, tssRegion=c(-3000, 3000), TxDb=txdb, genomicAnnotationPriority
updated 8.5 years ago • anupriyaverma1408
I realize this question has probably been asked a million times but I cannot find a case that's similar to mine.
I have 8 conditions but no reference. These are different strains of the same organism. I want to perform a pairwise comparison of all 8 groups , totaling 28 unique comparisons (no A vs. A, but A vs. B, A vs. C, etc..)
Is...s similar to mine.
I have 8 conditions but no refere…
updated 5.8 years ago • cnvspam
txdb <- makeTxDbFromGFF(file=gff.file.small, format="auto", dataSource=url,
organism="Vitis vinifera", taxonomyId=29760,
chrominfo=seqinfo(BSgenome.Vvinifera.URGI.IGGP12Xv0))
txdb # shows transcript_nrow
updated 9.7 years ago • TimothéeFlutre
Dear all,
I have carried out differential expression of RNA-seq data from a non-model organism using the limma+voom pipeline. Next, I wish to look for functional enrichment of DE genes using GOseq.
I successfully
updated 6.7 years ago • charles.foster
easyRNASeq(
filesDirectory=BamPath, filenames=fls.bam, nbCore=6, organism='Hsapiens', gapped = TRUE, annotationMethod="biomaRt", format="bam", count=c('genes'), outputFormat
updated 10.9 years ago • Mayte
<div class="preformatted">This two day course is described in a preliminary way at
https://github.com/vjcitn/bosBiocTrain . Registration form can also
be acquired at that site.
REGISTER BEFORE 1 OCTOBER AND DEDUCT 10% FROM REGISTRATION FEE.
Academic fee: $450; Commercial fee: $750. All proceeds are used
to defray expenses of room rental and to fund the activities of the
Bioconductor Fo…
updated 12.3 years ago • Vincent J. Carey, Jr.
the
GO semantic similarities between yeast proteins. Both of the two
packages work well on other organisms.
I use biomaRt package to map the Swiss Acc name to NCBI gene ID.
Unfortunately, when I use GOSemSim and GOSim package
Recent ...
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Answer: Limma-voom sample weights and impact on DEG numbers
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I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
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