Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
3
votes
8
replies
3.9k
views
Batch effects in limma
limma
batch effect
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
smt8n
• 0
0
votes
2
replies
1.6k
views
GCRMA segmentation fault
gcrma
segmentation
fault
segfault
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
kazi
• 0
0
votes
6
replies
2.6k
views
difficulty loading rsbml
rsbml
rsbml
updated 9.8 years ago by
den.kazakiewicz
• 0 • written 14.9 years ago by
Paul Shannon
★ 1.1k
2
votes
10
replies
3.0k
views
Package lists and other questions about the site
website
r packages
importing
9.8 years ago
george.carlisle
• 0
2
votes
2
replies
1.6k
views
limma making contrasts appropriately
limma
design and contrast matrix
updated 9.8 years ago by
Steve Lianoglou
★ 13k • written 9.8 years ago by
christopher.clarskon15
▴ 20
4
votes
6
replies
7.3k
views
goseq: not able to limit by GO categories when using wallenius approximation for over-representation test
goseq
updated 9.8 years ago by
Nadia Davidson
▴ 320 • written 9.8 years ago by
mrodrigues.fernanda
▴ 10
1
vote
2
replies
2.2k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
phil.chapman
▴ 150
1
vote
0
replies
1.5k
views
Job:
Industry Postdoc at EMBL: Statistical Computing in Multi-Omics and Drug Target Validation
job
Job
9.8 years ago
Wolfgang Huber
★ 13k
3
votes
2
replies
1.9k
views
Why does requireNamespace("org.Hs.eg.db") load DBI and RSQLite?
org.hs.eg.db
DBI
rsqlite
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
Gordon Smyth
53k
0
votes
5
replies
3.1k
views
How to get list of genes that are DE from the goseq analysis results
limma
goseq
mget
edgeR
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
darshinimamindla
▴ 10
2
votes
4
replies
2.6k
views
Error: could not find function "DMLtest"
dss
9.8 years ago
kafkaskid
▴ 20
4
votes
1
reply
6.6k
views
BPPARAM = bpparam() takes longer than using BPPARAM = SerialParam()
bplapply
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
benjamin.phillips22
▴ 10
4
votes
4
replies
2.6k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens
txdb
annotation
updated 9.8 years ago by
Valerie Obenchain
★ 6.8k • written 9.8 years ago by
enricoferrero
▴ 680
0
votes
1
reply
1.1k
views
plot Genome in aCGH
acgh
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
sainiisha22
• 0
1
vote
2
replies
1.3k
views
AnnotatedDataFrame crashes MS Visual Studio
affy
software error
9.8 years ago
Chris
• 0
0
votes
2
replies
3.5k
views
Odd Odds Ratio in GOstats package
GO
GOstats
GO
GOstats
updated 9.8 years ago by
bannistersc
• 0 • written 11.7 years ago by
Moreno Colaiacovo
▴ 10
2
votes
3
replies
3.1k
views
import.bed fails on bed file with no scores
rtracklayer
import
bed files
9.8 years ago
jmr
• 0
2
votes
4
replies
2.9k
views
goseq pwf length bias plot: help interpreting plot
goseq
updated 9.8 years ago by
Nadia Davidson
▴ 320 • written 9.8 years ago by
mrodrigues.fernanda
▴ 10
0
votes
2
replies
1.5k
views
negative value for minOverlap parameter
Rsubread
minOverlap
featureCounts
updated 9.8 years ago by
Wei Shi
★ 3.6k • written 9.8 years ago by
c.merce
• 0
7
votes
2
replies
2.0k
views
limma experimental design
limma
microarray
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
christopher.clarskon15
▴ 20
0
votes
1
reply
1.2k
views
Plot with two separated groups of genes.
scatter-plot
clustering
updated 9.8 years ago by
mrodrigues.fernanda
▴ 10 • written 9.8 years ago by
Adam
• 0
0
votes
0
replies
1.6k
views
Job:
Bioinformatics First Research Engineer position
bioinformatician job
next-generation sequencing
sweden
Job
9.8 years ago
Nicolas Delhomme
▴ 320
0
votes
0
replies
1.8k
views
Job:
Bioinformatics Research Engineer position
bioinformatician job
next-generation sequencing
sweden
Job
9.8 years ago
Nicolas Delhomme
▴ 320
5
votes
7
replies
2.1k
views
Co-expression between host and pathogen genes
edger
rna-seq
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
jhj89
▴ 10
0
votes
0
replies
1.3k
views
minfi dmpFinder input
minfi
9.8 years ago
igor
▴ 50
1
vote
3
replies
2.4k
views
Analyse of HGU133 set / Merge ExpressionSet
affy
hgu133a
hgu133b
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
giroudpaul
▴ 40
0
votes
1
reply
1.3k
views
Aditional undesired sample
phyloseq
9.8 years ago
sanrrone
• 0
3
votes
1
reply
2.4k
views
Not able to display actual grayscale image using EBImage
ebimage
image processing
image
display
updated 9.8 years ago by
Andrzej Oleś
▴ 750 • written 9.8 years ago by
Kpurva
▴ 10
1
vote
1
reply
2.0k
views
Differential binding using csaw
csaw
differential binding analysis
chipseq
differential expression
differential gene expression
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
Amitha Sampath
▴ 10
1
vote
9
replies
3.6k
views
Handling DNA sequence loaded from a file
r
biostrings
DNAsequence
updated 3.6 years ago by
James W. MacDonald
68k • written 9.8 years ago by
Agaz Hussain Wani
▴ 260
0
votes
2
replies
1.8k
views
GOstat GO term format "GO:00003567" or "3567" ?
GOstat
format
input files
9.8 years ago
bannistersc
• 0
3
votes
3
replies
1.9k
views
edgeR: cpm() behavior appears to depend on whether edgeR is exported into the namespace. Is this normal?
edgeR
namespace
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
BharathAnanth
▴ 80
0
votes
0
replies
1.1k
views
Package for classifying two classes of sequences using hidden markov models?
hmm
classification
9.8 years ago
vinod.acear
▴ 50
3
votes
15
replies
5.8k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
9.8 years ago
rasii
• 0
19
votes
4
replies
9.7k
views
Confidence intervals on edgeR logFC
edgeR
statistics
confidence interval
updated 9.8 years ago by
nwvidal
• 0 • written 11.3 years ago by
ri.lars
▴ 40
2
votes
4
replies
6.7k
views
Interaction terms in DESeq2 contrasts
deseq2
interactions
design and contrast matrix
contrast
9.8 years ago
dwzhang.wisc
▴ 20
5
votes
7
replies
3.2k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
chapmandu2
▴ 20
1
vote
8
replies
2.6k
views
SummarizedExperiment Error! expressionSet data structure
software error
summarizedexperiment
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
yifangt
▴ 20
3
votes
3
replies
1.5k
views
RNA-seq genes differentially expressed in combined treatment
DESeq2
deseq2
RNA-seq
9.8 years ago
david.ashbrook
• 0
1
vote
1
reply
1.9k
views
edgeR, DE between 4 different samples
edger
differential gene expression
GLM
Tutorial
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
wendy_11
• 0
0
votes
2
replies
1.3k
views
R version 3.3.0 beta crashing, how do I roll back?
software error
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
chris86
▴ 420
5
votes
8
replies
1.9k
views
designing matrices practice
limma
microarray
9.8 years ago
christopher.clarskon15
▴ 20
2
votes
2
replies
1.5k
views
goseq package: Is the package in sync with the most current Ensembl release?
goseq
ensembl
updated 9.8 years ago by
Johannes Rainer
★ 2.1k • written 9.8 years ago by
mrodrigues.fernanda
▴ 10
0
votes
1
reply
1.4k
views
plot pdf error
graph
updated 9.8 years ago by
Axel Klenk
★ 1.1k • written 9.8 years ago by
anu.kour
• 0
1
vote
3
replies
2.4k
views
bsseq BSmooth error
bsseq
9.8 years ago
enricoferrero
▴ 680
4
votes
3
replies
4.1k
views
limma: model/contrast matrix for 2x3 factorial design
limma
multifactorial design
design and contrast matrix
limma design matrix
limma contrast matrix
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
ckeeling
• 0
1
vote
1
reply
1.2k
views
Clustering like samples with a lot of data
clustering
9.8 years ago
gaiusjaugustus
• 0
0
votes
4
replies
5.7k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO
Category
goseq
GO
Category
goseq
updated 9.8 years ago by
darshinimamindla
▴ 10 • written 14.4 years ago by
Helen Wright
▴ 10
0
votes
2
replies
2.7k
views
Scaling fcs files with flowCore
flowCore
flowcytometry
9.8 years ago
Jiang, Mike
★ 1.3k
0
votes
6
replies
2.5k
views
Is that an efficient way to find the overlapped , upstream and downstream genes for a bunch of genes
genomicranges
geneoverlap
findoverlaps
updated 9.8 years ago by
Michael Lawrence
★ 11k • written 9.8 years ago by
yao.h.1988
• 0
46,721 results • Page
402 of 935
Recent ...
Replies
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Comment: Questions about bacon QC and correction on EWAS results
by
sup0903
• 0
This is qq plot and histogram generated before bacon correction ![enter image description here][1] ![enter image description here][2] …
Comment: Ensembl site unresponsive via biomaRt
by
sebastianenewell
• 0
> I think this is an unrelated issue. The original post includes the > message Error: 'curl_parse_url' is not an exported object from > 'na…
Comment: Development of MSstat workflow to analyze DIA time series data
by
Gordon Smyth
53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards
• All
Popular Question
to
maltethodberg
▴ 180
Popular Question
to
mohammedtoufiq91
▴ 10
Popular Question
to
Lluís Revilla Sancho
▴ 760
Commentator
to
James W. MacDonald
68k
Great Question
to
fl
▴ 20
Locations
• All
Pacific Ocean,
8 minutes ago
The city by the bay,
13 minutes ago
Denmark,
22 minutes ago
United Kingdom,
1 hour ago
South Korea,
1 hour ago
Traffic: 1611 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6