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15
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22
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1.8k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
25 days ago • updated 3 days ago
Chris
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 6 days ago
shepherl
3.8k
0
votes
18
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 20 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
1
vote
12
replies
196
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
updated 1 hour ago by
Guido Hooiveld
★ 3.9k • written 2 days ago by
fernanda.backsouza
▴ 10
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 1 day ago
shepherl
3.8k
12
votes
12
replies
745
views
Why p value inconsistent when using different number of pathway score?
limma
updated 2 days ago by
Robert Castelo
★ 3.3k • written 3 days ago by
Chris
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 5 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
5
votes
9
replies
844
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
13 days ago • updated 5 days ago
Chris
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 6 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
4
votes
8
replies
332
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 5 days ago by
Peter Hickey
▴ 740 • written 12 days ago by
Juan Higareda
• 0
5
votes
8
replies
8.7k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 1 day ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 6 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
0
votes
7
replies
236
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
7 days ago • updated 1 day ago
hortense96
• 0
0
votes
7
replies
604
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 17 hours ago
shepherl
3.8k
0
votes
7
replies
383
views
DESeq filtering specific to contrasts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
3
votes
6
replies
315
views
FilterByExpr low counts with small sample size
edgeR
6 days ago • updated 1 day ago
Jonathan
▴ 10
2
votes
5
replies
693
views
DESeq2 setting significant p-value
DESeq2
updated 4 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
6
votes
5
replies
392
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 6 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 5 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
188
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
6 days ago • updated 4 days ago
lonn
• 0
1
vote
4
replies
135
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 1 day ago by
James W. MacDonald
65k • written 5 days ago by
Mirella Aurora
• 0
0
votes
4
replies
160
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
2 days ago • updated 2 hours ago
Gayatri
• 0
1
vote
4
replies
117
views
minfi::read.metharray.exp
minfiData
minfi
updated 3 hours ago by
Basti
▴ 780 • written 1 day ago by
clacarion
• 0
0
votes
4
replies
126
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
5 days ago
sropri
• 0
0
votes
4
replies
227
views
DEG with low counts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 days ago by
Rajat
• 0
3
votes
3
replies
280
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 16 days ago by
Netanel
• 0
3
votes
3
replies
164
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
11 days ago • updated 6 days ago
jacques.imbert
• 0
1
vote
3
replies
775
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 1 hour ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
0
votes
3
replies
220
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 5 days ago by
W. Evan Johnson
▴ 850 • written 12 days ago by
schlumbohm
• 0
0
votes
3
replies
95
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
bas_work
▴ 30
3
votes
3
replies
139
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 21 hours ago by
Michael Love
41k • written 1 day ago by
WardDeb
• 0
0
votes
3
replies
66
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 2 hours ago by
ATpoint
★ 4.0k • written 19 hours ago by
Aaliya
• 0
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 2 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
3
replies
124
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
prity6459
• 0
1
vote
2
replies
42
views
get BM error
ensembldb
4 hours ago • updated 3 hours ago
Fara
• 0
0
votes
2
replies
884
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 6 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
2
replies
123
views
Error in champ.load(): The following specified files do not exist
ChAMP
6 days ago • updated 5 days ago
Sherin
• 0
1
vote
2
replies
177
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 days ago • updated 5 days ago
Le
• 0
0
votes
2
replies
896
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
85
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
5 days ago
prity6459
• 0
2
votes
2
replies
133
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
sansan
• 0
0
votes
2
replies
233
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
23 days ago • updated 4 days ago
isaac.vock
• 0
1
vote
2
replies
215
views
How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago
Weiqian
▴ 10
0
votes
2
replies
763
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 7 months ago by
Gordon Smyth
50k
0
votes
2
replies
142
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 days ago • updated 2 days ago
catv
• 0
3
votes
2
replies
143
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 1 day ago by
Guido Hooiveld
★ 3.9k • written 4 days ago by
fernanda.backsouza
▴ 10
1
vote
2
replies
915
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 1 day ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
76 results • Page
1 of 2
Recent ...
Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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