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15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 4 days ago
Chris
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
14 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 16 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
8
votes
23
replies
933
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 22 days ago by
Robert Castelo
★ 3.3k • written 24 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
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 15 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
6
votes
5
replies
430
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 9 weeks ago by
Kim
• 0
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 4 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 12 days ago
shepherl
3.9k
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
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
916
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
23 days ago • updated 16 days ago
Chris
• 0
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
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
5
votes
25
replies
902
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
6
replies
423
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 21 days ago by
ATpoint
★ 4.1k • written 25 days ago by
nhaus
▴ 30
4
votes
6
replies
418
views
FilterByExpr low counts with small sample size
edgeR
16 days ago • updated 11 days ago
Jonathan
▴ 10
4
votes
8
replies
389
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 15 days ago by
Peter Hickey
▴ 740 • written 23 days ago by
Juan Higareda
• 0
3
votes
1
reply
167
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
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
207
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
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
3
votes
4
replies
190
views
Help with error using camera() in limma
CAMERA
limma
4 days ago • updated 3 days ago
Chris
• 0
3
votes
0
replies
52
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
2 days ago
shepherl
3.9k
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
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
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
23 days ago
nhaus
▴ 30
3
votes
3
replies
200
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
22 days ago • updated 16 days ago
jacques.imbert
• 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
3
replies
220
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
WardDeb
• 0
3
votes
2
replies
209
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 12 days ago by
Guido Hooiveld
★ 3.9k • written 14 days ago by
fernanda.backsouza
▴ 10
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
2
replies
183
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
sansan
• 0
2
votes
5
replies
744
views
DESeq2 setting significant p-value
DESeq2
updated 15 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
177
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
190
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 29 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Dario Strbenac
★ 1.5k
2
votes
5
replies
253
views
get BM error
ensembldb
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
Fara
• 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
22 days ago • updated 21 days ago
julia_mcdonough
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 17 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
2
replies
170
views
[DiffBind] Obtaining normalization factors
DiffBind
21 days ago • updated 18 days ago
Henry
▴ 10
2
votes
5
replies
229
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
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
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
102
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 20 hours ago by
Michael Love
41k • written 20 hours ago by
Reza
• 0
2
votes
2
replies
168
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
22 days ago • updated 19 days ago
daniel.carbajo
• 0
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
9
replies
362
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 9 days ago by
Alexandre
• 0
2
votes
2
replies
386
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
22 days ago • updated 21 days ago
Henry
▴ 10
1
vote
4
replies
201
views
minfi::read.metharray.exp
minfiData
minfi
updated 10 days ago by
Basti
▴ 780 • written 12 days ago by
clacarion
• 0
200 results • Page
1 of 4
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
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