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15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
29 days ago • updated 7 days ago
Chris
• 0
12
votes
13
replies
815
views
Why p value inconsistent when using different number of pathway score?
limma
7 days ago • updated 21 minutes ago
Chris
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 8 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 9 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
8
votes
23
replies
871
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 16 days ago by
Robert Castelo
★ 3.3k • written 17 days ago by
Bine
▴ 40
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 23 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 13 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
6
votes
16
replies
2.3k
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
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 8 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 5 days ago
shepherl
3.8k
6
votes
5
replies
399
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
5
votes
6
replies
400
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 14 days ago by
ATpoint
★ 4.0k • written 18 days ago by
nhaus
▴ 30
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 9 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
9
replies
869
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
16 days ago • updated 9 days ago
Chris
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 4 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
25
replies
832
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 22 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jitendra
▴ 10
4
votes
6
replies
356
views
FilterByExpr low counts with small sample size
edgeR
10 days ago • updated 5 days ago
Jonathan
▴ 10
4
votes
8
replies
360
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 8 days ago by
Peter Hickey
▴ 740 • written 16 days ago by
Juan Higareda
• 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
1
reply
128
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 8 days ago by
Gordon Smyth
50k • written 9 days ago by
Shaimaa Gamal
• 0
3
votes
5
replies
351
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 27 days ago by
Gordon Smyth
50k • written 29 days ago by
Fabian
• 0
3
votes
3
replies
179
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
15 days ago • updated 9 days ago
jacques.imbert
• 0
3
votes
6
replies
239
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
16 days ago
nhaus
▴ 30
3
votes
1
reply
235
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
i.sudbery
▴ 40
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 10 days ago
shepherl
3.8k
3
votes
2
replies
171
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 7 days ago by
fernanda.backsouza
▴ 10
3
votes
3
replies
179
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
WardDeb
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 23 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
3
votes
3
replies
295
views
permutation test in edgeR
rna-seq
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 19 days ago by
Netanel
• 0
3
votes
1
reply
748
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
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 24 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
2
votes
5
replies
705
views
DESeq2 setting significant p-value
DESeq2
updated 8 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
363
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
16 days ago • updated 15 days ago
Henry
▴ 10
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 27 days ago by
isaac.vock
• 0 • written 7.9 years ago by
Jon Manning
▴ 90
2
votes
9
replies
281
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
Alexandre
• 0
2
votes
2
replies
146
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
sansan
• 0
2
votes
2
replies
153
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
15 days ago • updated 12 days ago
daniel.carbajo
• 0
2
votes
2
replies
151
views
[DiffBind] Obtaining normalization factors
DiffBind
15 days ago • updated 11 days ago
Henry
▴ 10
2
votes
2
replies
175
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
15 days ago • updated 14 days ago
julia_mcdonough
• 0
2
votes
6
replies
358
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
19 days ago
Chris
• 0
2
votes
2
replies
171
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 22 days ago by
ATpoint
★ 4.0k • written 22 days ago by
Dario Strbenac
★ 1.5k
2
votes
5
replies
167
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
bandconductor
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 10 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
176
views
get BM error
ensembldb
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
Fara
• 0
2
votes
3
replies
298
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
12 days ago • updated 11 days ago
daniel.carbajo
• 0
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 22 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
1
vote
3
replies
122
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 day ago by
Michael Love
41k • written 1 day ago by
JalapenoCornbread
• 0
1
vote
3
replies
137
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 23 days ago by
Michael Love
41k • written 24 days ago by
RL
• 0
1
vote
13
replies
305
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
6 days ago • updated 2 days ago
fernanda.backsouza
▴ 10
194 results • Page
1 of 4
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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