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
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 3 days ago
Chris
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
13 days ago • updated 2 days ago
Chris
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 15 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 15 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
8
votes
23
replies
932
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 22 days ago by
Robert Castelo
★ 3.3k • written 23 days ago by
Bine
▴ 40
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 29 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 11 days ago
shepherl
3.9k
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
6
votes
5
replies
429
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 9 weeks ago by
Kim
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 20 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 14 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 11 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 16 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
25
replies
895
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 29 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
5
votes
9
replies
909
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
23 days ago • updated 15 days ago
Chris
• 0
5
votes
6
replies
423
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 21 days ago by
ATpoint
★ 4.1k • written 24 days ago by
nhaus
▴ 30
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 1 day ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
4
votes
6
replies
416
views
FilterByExpr low counts with small sample size
edgeR
16 days ago • updated 11 days ago
Jonathan
▴ 10
4
votes
8
replies
387
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 15 days ago by
Peter Hickey
▴ 740 • written 22 days ago by
Juan Higareda
• 0
3
votes
1
reply
302
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
i.sudbery
▴ 40
3
votes
3
replies
206
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
bioinf
▴ 10
3
votes
1
reply
166
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 15 days ago by
Gordon Smyth
50k • written 16 days ago by
Shaimaa Gamal
• 0
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 16 days ago
shepherl
3.9k
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
3
votes
3
replies
327
views
permutation test in edgeR
rna-seq
edgeR
updated 13 days ago by
Gordon Smyth
50k • written 26 days ago by
Netanel
• 0
3
votes
3
replies
197
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
21 days ago • updated 16 days ago
jacques.imbert
• 0
3
votes
0
replies
50
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
2 days ago
shepherl
3.9k
3
votes
3
replies
219
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 days ago by
WardDeb
• 0
3
votes
2
replies
207
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 11 days ago by
Guido Hooiveld
★ 3.9k • written 14 days ago by
fernanda.backsouza
▴ 10
3
votes
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
22 days ago
nhaus
▴ 30
3
votes
4
replies
188
views
Help with error using camera() in limma
CAMERA
limma
3 days ago
Chris
• 0
3
votes
1
reply
753
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 29 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
2
votes
5
replies
744
views
DESeq2 setting significant p-value
DESeq2
updated 14 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
183
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
sansan
• 0
2
votes
2
replies
190
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
21 days ago
julia_mcdonough
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 16 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
227
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 8 days ago by
James W. MacDonald
65k • written 10 days ago by
bandconductor
• 0
2
votes
6
replies
397
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
25 days ago
Chris
• 0
2
votes
9
replies
356
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
Alexandre
• 0
2
votes
2
replies
176
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
4 days ago
Chris
• 0
2
votes
2
replies
170
views
[DiffBind] Obtaining normalization factors
DiffBind
21 days ago • updated 18 days ago
Henry
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 3 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
2
votes
2
replies
188
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 28 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Dario Strbenac
★ 1.5k
2
votes
2
replies
96
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 14 hours ago by
Michael Love
41k • written 15 hours ago by
Reza
• 0
2
votes
2
replies
384
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
22 days ago • updated 21 days ago
Henry
▴ 10
2
votes
2
replies
168
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
21 days ago • updated 19 days ago
daniel.carbajo
• 0
2
votes
5
replies
249
views
get BM error
ensembldb
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
Fara
• 0
2
votes
3
replies
321
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
19 days ago • updated 18 days ago
daniel.carbajo
• 0
202 results • Page
1 of 5
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
• 0
Popular Question
to
Theo
▴ 10
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Locations
• All
France,
1 minute ago
Miami, FL,
17 minutes ago
WEHI, Melbourne, Australia,
35 minutes ago
Sweden,
52 minutes ago
Japan,
1 hour ago
Traffic: 415 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