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2
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4
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110
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How to retrieve gene ontology GO class from gene list?
GO.db
goTools
1 day ago • updated 41 minutes ago
bandconductor
• 0
0
votes
4
replies
290
views
Help with design.matrix
limma
19 days ago • updated 18 days ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
129
views
minfi::read.metharray.exp
minfiData
minfi
updated 1 day ago by
Basti
▴ 780 • written 3 days ago by
clacarion
• 0
0
votes
4
replies
568
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 8 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
4
replies
392
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
24 days ago • updated 23 days ago
Lucy
▴ 60
1
vote
4
replies
60
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 1 hour ago by
James W. MacDonald
65k • written 3 hours ago by
Alexandre
• 0
0
votes
4
replies
131
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago
sropri
• 0
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
0
votes
4
replies
3.9k
views
SingleR Label.Ont
SingleR
updated 9 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
4
replies
199
views
Storing directories inside an ExperimentHub package?
ExperimentHub
14 days ago • updated 13 days ago
Tim Barry
• 0
0
votes
4
replies
153
views
flowStats Search Error
flowStats
updated 8 days ago by
shepherl
3.8k • written 9 days ago by
tholmes
• 0
1
vote
4
replies
143
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 2 days ago by
James W. MacDonald
65k • written 6 days ago by
Mirella Aurora
• 0
0
votes
4
replies
232
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by
Michael Love
41k • written 23 days ago by
Aidan
• 0
1
vote
4
replies
413
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 days ago by
Gordon Smyth
50k • written 22 days ago by
jari.karppinen
• 0
5
votes
3
replies
684
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 28 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jack S.
▴ 50
2
votes
3
replies
293
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
10 days ago • updated 9 days ago
daniel.carbajo
• 0
0
votes
3
replies
102
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
bas_work
▴ 30
1
vote
3
replies
87
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
3
replies
107
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 2 hours ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
3
votes
3
replies
156
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
2
votes
3
replies
324
views
PCA of different bacterial species
DESeq2
updated 29 days ago by
Michael Love
41k • written 29 days ago by
Laura
▴ 10
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 21 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
3
replies
312
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
3
votes
3
replies
285
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 17 days ago by
Netanel
• 0
0
votes
3
replies
223
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 days ago by
W. Evan Johnson
▴ 850 • written 13 days ago by
schlumbohm
• 0
1
vote
3
replies
811
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 1 day ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
3
votes
3
replies
169
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
13 days ago • updated 7 days ago
jacques.imbert
• 0
0
votes
3
replies
128
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
prity6459
• 0
1
vote
3
replies
252
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 28 days ago by
mercedeh.movassagh
▴ 10 • written 5 weeks ago by
María
• 0
1
vote
3
replies
228
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 19 days ago by
James W. MacDonald
65k • written 20 days ago by
Shaimaa Gamal
• 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
320
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 10 days ago by
Gordon Smyth
50k • written 15 days ago by
Simran
• 0
0
votes
2
replies
898
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
237
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
24 days ago • updated 6 days ago
isaac.vock
• 0
1
vote
2
replies
212
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 29 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
739
views
error in install immunedeconv
Install
updated 21 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
0
votes
2
replies
166
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
24 days ago • updated 23 days ago
Seongsu
• 0
1
vote
2
replies
218
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
4 weeks ago • updated 29 days ago
Mj.A.
• 0
0
votes
2
replies
886
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 7 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 12.4 years ago by
Bogdan
▴ 670
0
votes
2
replies
165
views
Gene Ontology doubt
microbiomeExplorer
24 days ago • updated 20 days ago
Bhawna
• 0
0
votes
2
replies
146
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
22 days ago
Marianna
▴ 20
0
votes
2
replies
276
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
24 days ago • updated 19 days ago
fer_talavera
• 0
2
votes
2
replies
146
views
[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 9 days ago
Henry
▴ 10
2
votes
2
replies
170
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 20 days ago by
ATpoint
★ 4.0k • written 20 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
193
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 15 days ago by
Michael Love
41k • written 20 days ago by
nhaus
▴ 30
2
votes
2
replies
146
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
13 days ago • updated 10 days ago
daniel.carbajo
• 0
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 28 days ago by
hortense96
• 0 • written 6.3 years ago by
a.mcneill
• 0
1
vote
2
replies
370
views
GSVA error
GSVA
11 days ago • updated 10 days ago
Alex
• 0
203 results • Page
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Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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