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15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 5 days ago
Chris
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
15 days ago • updated 4 days ago
Chris
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 17 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 17 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
8
votes
23
replies
947
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 24 days ago by
Robert Castelo
★ 3.3k • written 25 days ago by
Bine
▴ 40
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 hours ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
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 5 days ago by
Sey R.
• 0 • 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 16 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 13 days ago
shepherl
3.9k
6
votes
5
replies
437
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 22 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
5
votes
6
replies
426
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 23 days ago by
ATpoint
★ 4.1k • written 26 days ago by
nhaus
▴ 30
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 18 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
9
replies
928
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
25 days ago • updated 17 days ago
Chris
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 13 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 3 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
4
votes
6
replies
430
views
FilterByExpr low counts with small sample size
edgeR
18 days ago • updated 13 days ago
Jonathan
▴ 10
4
votes
8
replies
396
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 17 days ago by
Peter Hickey
▴ 740 • written 25 days ago by
Juan Higareda
• 0
3
votes
1
reply
177
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 17 days ago by
Gordon Smyth
50k • written 18 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
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 18 days ago
shepherl
3.9k
3
votes
3
replies
336
views
permutation test in edgeR
rna-seq
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 28 days ago by
Netanel
• 0
3
votes
3
replies
205
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
23 days ago • updated 18 days ago
jacques.imbert
• 0
3
votes
3
replies
228
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
bioinf
▴ 10
3
votes
4
replies
204
views
Help with error using camera() in limma
CAMERA
limma
5 days ago
Chris
• 0
3
votes
0
replies
68
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
4 days ago
shepherl
3.9k
3
votes
6
replies
273
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
25 days ago • updated 24 days ago
nhaus
▴ 30
3
votes
1
reply
467
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 7 hours ago by
Gordon Smyth
50k • written 3 days ago by
gene_bioconductor
▴ 10
3
votes
1
reply
755
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
1
reply
312
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by
Michael Love
41k • written 12 days ago by
i.sudbery
▴ 40
3
votes
3
replies
227
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by
Michael Love
41k • written 13 days ago by
WardDeb
• 0
3
votes
2
replies
216
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 14 days ago by
Guido Hooiveld
★ 3.9k • written 16 days ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
98
views
fgsea significant result
fgsea
1 day ago • updated 17 hours ago
Chris
• 0
2
votes
3
replies
158
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
Reza
• 0
2
votes
6
replies
401
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
27 days ago
Chris
• 0
2
votes
5
replies
750
views
DESeq2 setting significant p-value
DESeq2
updated 16 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
389
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
24 days ago • updated 23 days ago
Henry
▴ 10
2
votes
3
replies
328
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
21 days ago • updated 20 days ago
daniel.carbajo
• 0
2
votes
3
replies
133
views
package goseq seems to be not available on the latest version of R
goseq
updated 46 minutes ago by
Gordon Smyth
50k • written 2 days ago by
Patrycja
▴ 20
2
votes
2
replies
172
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
24 days ago • updated 21 days ago
daniel.carbajo
• 0
2
votes
2
replies
191
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
6 days ago
Chris
• 0
2
votes
2
replies
171
views
[DiffBind] Obtaining normalization factors
DiffBind
23 days ago • updated 20 days ago
Henry
▴ 10
2
votes
2
replies
190
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
sansan
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 18 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
240
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 10 days ago by
James W. MacDonald
65k • written 12 days ago by
bandconductor
• 0
2
votes
9
replies
389
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Alexandre
• 0
2
votes
2
replies
193
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
23 days ago
julia_mcdonough
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 5 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
2
votes
5
replies
264
views
get BM error
ensembldb
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
Fara
• 0
1
vote
3
replies
861
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 12 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
191 results • Page
1 of 4
Recent ...
Replies
Comment: Couldn't connect to server while using "pathways"
by
ATpoint
★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of unavailability.…
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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