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Why p value inconsistent when using different number of pathway score?
limma
updated 57 minutes ago by
ATpoint
★ 4.0k • written 2 hours ago by
Chris
• 0
0
votes
0
replies
9
views
I am trying to detect alternative splicing but getting error.
ASpli
3 hours ago
Sebashish
• 0
0
votes
0
replies
10
views
I am trying to detect alternative splicing.
ASpli
3 hours ago
Sebashish
• 0
0
votes
1
reply
62
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 16 hours ago by
deeenes
▴ 30 • written 19 hours ago by
fernanda.backsouza
• 0
0
votes
1
reply
58
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
updated 17 hours ago by
Gordon Smyth
50k • written 1 day ago by
catv
• 0
0
votes
0
replies
31
views
FDR via q-value
qvalue
23 hours ago
John
• 0
0
votes
6
replies
564
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 1 day ago
shepherl
3.8k
0
votes
3
replies
59
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
bas_work
▴ 30
1
vote
2
replies
78
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
sansan
• 0
1
vote
0
replies
112
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
1 day ago • updated 23 hours ago
BioinfGuru
▴ 30
0
votes
4
replies
198
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 1 day ago
Jonathan
▴ 10
0
votes
2
replies
59
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
1 day ago
prity6459
• 0
0
votes
3
replies
83
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
prity6459
• 0
0
votes
1
reply
75
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
89
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
1 day ago
sropri
• 0
0
votes
0
replies
33
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
1 day ago
Mirella Aurora
• 0
0
votes
1
reply
55
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 2 days ago by
Alessia
• 0
0
votes
1
reply
87
views
Adding columns to DEXSeqResults object
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Clyde
• 0
0
votes
0
replies
50
views
Warning while loading DEP package
DEP
updated 2 days ago by
shepherl
3.8k • written 2 days ago by
Namrata
• 0
0
votes
1
reply
59
views
rlog transformation
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
ishij9717
• 0
0
votes
1
reply
56
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 2 days ago by
Michael Love
41k • written 2 days ago by
09191919
• 0
0
votes
1
reply
65
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
ussarizona
• 0
0
votes
1
reply
82
views
covariate with negative and positive values
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
Brynn
• 0
0
votes
1
reply
84
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 3 days ago by
quanah.hudson
• 0
1
vote
2
replies
150
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
2 days ago • updated 1 day ago
Le
• 0
1
vote
2
replies
99
views
Error in champ.load(): The following specified files do not exist
ChAMP
2 days ago
Sherin
• 0
0
votes
1
reply
59
views
Input Question for deseq.r
RSeqAn
updated 2 days ago by
ATpoint
★ 4.0k • written 2 days ago by
Nina
• 0
0
votes
4
replies
142
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
3 days ago • updated 10 hours ago
lonn
• 0
0
votes
6
replies
163
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
hortense96
• 0
0
votes
0
replies
43
views
News:
Services
flowBeads
3 days ago
creativepeptides2018
• 0
0
votes
0
replies
34
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Enzyme Engineering
BioTIP
3 days ago
bocchemistry
• 0
0
votes
0
replies
45
views
News:
TIDES USA 2024
flowBeads
3 days ago
bocsci11
• 0
0
votes
0
replies
55
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
3 days ago
Maliha Tabassum
• 0
0
votes
4
replies
125
views
flowStats Search Error
flowStats
updated 3 days ago by
shepherl
3.8k • written 4 days ago by
tholmes
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 2 days ago
shepherl
3.8k
0
votes
1
reply
98
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 4 days ago by
James W. MacDonald
65k • written 6 days ago by
tian.liu0720
• 0
1
vote
2
replies
89
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
4 days ago
Ana
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
80
views
what is the sampleFiles
chipseq
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
zhulin
• 0
0
votes
1
reply
120
views
Differentially expressed genes in monocle pseudotime
monocle
updated 4 days ago by
Gordon Smyth
50k • written 6 days ago by
kthapa
• 0
4
votes
8
replies
312
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 1 day ago by
Peter Hickey
▴ 740 • written 9 days ago by
Juan Higareda
• 0
3
votes
3
replies
146
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
8 days ago • updated 2 days ago
jacques.imbert
• 0
0
votes
1
reply
110
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 4 days ago by
kamryncole1963
• 0 • written 9 days ago by
Sara
• 0
0
votes
3
replies
151
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
66
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 days ago
Virangika
• 0
0
votes
0
replies
49
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
5 days ago
Henry
▴ 10
1
vote
2
replies
200
views
How to retrieve detailed regression results from deseq2
DESeq2
9 days ago • updated 21 hours ago
Weiqian
▴ 10
0
votes
4
replies
205
views
DEG with low counts
DESeq2
updated 1 day ago by
Michael Love
41k • written 5 days ago by
Rajat
• 0
1
vote
2
replies
241
views
GSVA error
GSVA
6 days ago • updated 5 days ago
Alex
• 0
2
votes
3
replies
267
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
5 days ago • updated 4 days ago
daniel.carbajo
• 0
45,554 results • Page
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Recent ...
Replies
Answer: Why p value inconsistent when using different number of pathway score?
by
ATpoint
★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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