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
0
votes
2
replies
1.2k
views
GRangesList: wiered error
genomicranges
genomicfeatures
8.2 years ago
Fabian Grammes
▴ 20
2
votes
6
replies
1.8k
views
Running DESeq2 with gene-dependent binary variable such as membership in pathway?
deseq2
updated 8.2 years ago by
indradhawa1562
• 0 • written 8.2 years ago by
yuri.pritykin
• 0
0
votes
0
replies
1.2k
views
Recurring error in smoothMethygenoset step for MethyAnalysis
methyanalysis
8.2 years ago
charleneee95
• 0
3
votes
5
replies
3.7k
views
Found more than one class
r
bioconductor
8.2 years ago
Kamil Slowikowski
▴ 30
1
vote
7
replies
3.1k
views
Cannot retrieve projects from TCGA using getGDCprojects function
tcgabiolinks
TCGA
software error
8.2 years ago
jacorvar
▴ 40
0
votes
0
replies
1.6k
views
Job:
Postdoc in Computational Biology/Bioinformatics, IMB Mainz, Germany
job
bioinformatics
germany
Job
8.2 years ago
Mario Dejung
• 0
1
vote
2
replies
2.1k
views
Reading fastq file after narrowing sequences
ShortRead
FastqStreamer
8.2 years ago
ioannis.vardaxis
▴ 30
0
votes
2
replies
2.6k
views
Differential expression between multiple groups
multiple groups
differential gene expression
microarray
8.2 years ago
A
▴ 60
0
votes
1
reply
7.0k
views
Calling differential peaks from ATAC-seq data using DEseq2
deseq2
atac-seq
updated 8.2 years ago by
Rory Stark
★ 5.2k • written 8.2 years ago by
zhongjixx
• 0
3
votes
6
replies
3.0k
views
Standardizing gene symbols
R
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
Nithisha
▴ 10
0
votes
0
replies
2.1k
views
Merge two BAM files into one paired-end file
paired-end reads
bam file
8.2 years ago
ioannis.vardaxis
▴ 30
5
votes
6
replies
6.6k
views
Analyzing data without replicates using DiffBind
diffbind
bioconductor
differential binding analysis
without replicate
chipseq
8.2 years ago
Hesh
▴ 10
0
votes
5
replies
2.1k
views
403 Forbidden During Install
bioconductor
updated 8.2 years ago by
Valerie Obenchain
★ 6.8k • written 8.2 years ago by
jjrozewicki
• 0
1
vote
1
reply
2.0k
views
Trying to annotate microarray data and some probe set presents mismatch
annotation
affymetrix microarrays
updated 8.2 years ago by
James W. MacDonald
68k • written 8.2 years ago by
arronar
• 0
1
vote
7
replies
5.6k
views
deseq2 analysis with multiple factors and interaction terms
deseq2
multiple factor design
differential analysis
differential gene expression
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
hsbio
▴ 10
5
votes
9
replies
4.1k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 2.4 years ago by
Novice_cam
• 0 • written 8.2 years ago by
knaxerova
▴ 10
2
votes
2
replies
2.5k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport
limma
rna-seq
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
Ahdee
▴ 60
1
vote
3
replies
2.1k
views
Boxplot and Identification of DEG
limma
biobase
geoquery
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
nia
▴ 20
1
vote
3
replies
1.4k
views
Time-course group difference analysis with repeated individuals using limma-voom
limma
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
Leonardo Collado Torres
★ 1.1k
0
votes
0
replies
1.0k
views
DEXSeq : Preprocessing within R for Forward-Reverse Library
DEXSeq
8.2 years ago
ZheFrench
▴ 60
0
votes
2
replies
1.7k
views
Unable to load sqlite file generated by Cuffdiff
cuffdiff
sqlite
8.2 years ago
handgabriel
• 0
0
votes
1
reply
3.6k
views
gseaplot() function of clusterProfiler went wrong
gsea
clusterprofiler
8.2 years ago
giuseppe0525
• 0
0
votes
1
reply
1.6k
views
Solve overlapping gene labels in volcano plot when using textxy
R
8.2 years ago
Nithisha
▴ 10
0
votes
0
replies
732
views
Column name mismatch
software error
8.2 years ago
zuolin.bai
• 0
0
votes
1
reply
1.4k
views
Running DESeq2 on top variable genes?
deseq2
variance
genes
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
hs.lansdell
▴ 20
0
votes
3
replies
1.5k
views
Design matrix for longitudinal discordant twin analysis with limma
limma
limma design matrix
limma paired analysis
twin analysis
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
ist
• 0
2
votes
1
reply
1.9k
views
derfinder mean Expressed Region cutoff
derfinder
updated 8.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 8.2 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
0
replies
986
views
Bugs in HTqPCR 1.30.0?
htqpcr
8.2 years ago
h.roest
• 0
0
votes
1
reply
2.0k
views
DESeq2, lfcShrink, "Error in results(dds.shr, name = coefAlpha) : object 'coefAlpha' not found"
deseq2
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
lychen83
• 0
0
votes
7
replies
2.0k
views
Model matrix not full rank for condition-time experiment
Model matrix not full rank
deseq2
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
sally_b86
• 0
0
votes
1
reply
1.8k
views
Multi Anova in DESeq2
deseq2
updated 8.2 years ago by
Michael Love
43k • written 8.9 years ago by
denius
• 0
0
votes
1
reply
2.4k
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, ?
deseq2
filter
genefilter
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
Björn
• 0
0
votes
4
replies
2.2k
views
Time points and donors - errors with contrasts
deseq2
contrast
updated 8.2 years ago by
Michael Love
43k • written 8.5 years ago by
sasha
• 0
0
votes
1
reply
3.3k
views
Normalize depth before calculating TPM
rna-seq
TPM
library size factor
8.2 years ago
colore
• 0
0
votes
3
replies
5.2k
views
Error while processing BAM file with Picard FixMateInformation
diffHic
diffhic
updated 8.2 years ago by
geryk.jan
• 0 • written 10.2 years ago by
koustav.pal
• 0
1
vote
2
replies
1.8k
views
No differential expression with limmaCtData possible
limma
htqpcr
8.2 years ago
h.roest
• 0
0
votes
0
replies
1.6k
views
invalid names for slots of class GOHyperGResult
gostats
8.2 years ago
laianavarromartin
▴ 20
0
votes
0
replies
944
views
interGeneCorrelation and voom
voom
interGeneCorrelation
limma
8.2 years ago
maltethodberg
▴ 180
0
votes
4
replies
9.2k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo
annotate
8.2 years ago
llkxiaolan
▴ 10
5
votes
3
replies
5.2k
views
Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
homo.sapiens
annotationdbi
updated 8.2 years ago by
Johannes Rainer
★ 2.1k • written 8.2 years ago by
Shian Su
▴ 40
1
vote
1
reply
2.0k
views
Highlight ECs by KEGG module
pathview
KEGG
updated 8.2 years ago by
Luo Weijun
★ 1.6k • written 8.2 years ago by
wrodriguez
• 0
0
votes
3
replies
2.5k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2
ruvseq
rna-seq
batch effect
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
dbouzo
• 0
2
votes
3
replies
2.2k
views
GenomicRanges_RaggedExperiment Error in as background, class mcol no method or default for coercing logical to factor
genomicranges
RaggedExperiment
coercion
logical
factor
updated 8.2 years ago by
Marcel Ramos
700 • written 8.2 years ago by
Taran
• 0
0
votes
2
replies
24k
views
Determining gene expression levels with DESeq2 in a design with no condition
deseq2
tcga
8.2 years ago
robles.daniela
• 0
1
vote
2
replies
2.4k
views
DESeq2 for differential gene expression on GTEx dataset
rnaseq
deseq2
gtex
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
vikram
• 0
2
votes
6
replies
16k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
8.2 years ago
giuseppe0525
• 0
0
votes
2
replies
1.6k
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind
dba.report
filtering
8.2 years ago
konstantopoulos
• 0
1
vote
1
reply
1.9k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 8.2 years ago by
k.vitting.seerup
▴ 120 • written 8.2 years ago by
amy16
• 0
1
vote
4
replies
2.6k
views
cran check shows that genefilter is not available
genefilter
8.2 years ago
jinkaixiu
▴ 10
0
votes
1
reply
1.6k
views
Reference annotation file contains only transcript and CDS information, how to analyze the different expression of genes?
transcription
hisat2
8.2 years ago
zoukai3412085
• 0
46,726 results • Page
296 of 935
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Awards
• All
Popular Question
to
Lluís Revilla Sancho
▴ 760
Popular Question
to
nromerov
• 0
Popular Question
to
Thomas Girke
★ 1.7k
Teacher
to
Gordon Smyth
53k
Popular Question
to
Stephanie M. Gogarten
▴ 890
Locations
• All
WEHI, Melbourne, Australia,
1 hour ago
United States,
1 hour ago
United States,
2 hours ago
Chile,
4 hours ago
The city by the bay,
5 hours ago
Traffic: 951 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