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38
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QSEA:Error in h(simpleError(msg, call))
qsea
9 hours ago • updated 8 hours ago
kf
• 0
2
votes
1
reply
48
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 11 hours ago by
James W. MacDonald
67k • written 12 hours ago by
rae.alshammari
▴ 10
1
vote
3
replies
162
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO
clusterProfiler
enr
updated 13 hours ago by
James W. MacDonald
67k • written 16 hours ago by
Fatima
• 0
0
votes
6
replies
132
views
When doing differential methylation using the sesame package, seems to only go one way
methylation
sesame
methylationArrayAnalysis
1 day ago • updated 6 hours ago
ramiro.barrantes
▴ 10
0
votes
0
replies
34
views
Mark seleced variables in the x-loading plot
OPLS
genomes
Proteomics
21 hours ago
Ragnhild
• 0
0
votes
0
replies
29
views
News:
Metabolomics with R/Bioconductor Online Course
metabomxtr
MetaboCoreUtils
metabolomicsWorkbenchR
Metabolomics
1 day ago
info
▴ 10
2
votes
1
reply
63
views
object 'hdac_targets' not found
TPP
updated 1 day ago by
James W. MacDonald
67k • written 1 day ago by
Alexandre Mahé
• 0
0
votes
1
reply
60
views
KEGGgraph result difference
igraph
KEGGgraph
RCy3
GraphNEL
updated 1 day ago by
alex.pico
▴ 20 • written 1 day ago by
Arindam
▴ 80
0
votes
0
replies
40
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings
packageinstallation
1 day ago
semra
• 0
1
vote
2
replies
172
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray
methylation
sesame
methylationArrayAnalysis
2 days ago • updated 1 day ago
ramiro.barrantes
▴ 10
0
votes
1
reply
61
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 1 day ago by
Lluís Revilla Sancho
▴ 730 • written 1 day ago by
emilymily77
• 0
1
vote
2
replies
114
views
WARNING: No Bioconductor dependencies detected.
Bioconductor
Biocon
3 days ago • updated 1 day ago
katja.danielzik
• 0
0
votes
3
replies
206
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 1 day ago by
Yang Liao
▴ 440 • written 2 days ago by
venusian.martin
• 0
0
votes
1
reply
66
views
Annotating DMRs
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 2 days ago by
James W. MacDonald
67k • written 2 days ago by
ramiro.barrantes
▴ 10
0
votes
2
replies
251
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 4 days ago by
swbarnes2
★ 1.4k • written 9 days ago by
Megan
• 0
0
votes
2
replies
154
views
concentration tables suitable as input for new packages?
Bioconductor
4 days ago • updated 3 days ago
katja.danielzik
• 0
2
votes
0
replies
112
views
News:
Save the Date for EuroBioC2025 in Barcelona!
EuroBioC2025
Conference
Bioconductor
Community
4 days ago
Maria Doyle
▴ 90
0
votes
1
reply
86
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 2 days ago by
James W. MacDonald
67k • written 4 days ago by
bioinformaticssrm2011
• 0
0
votes
5
replies
1.5k
views
DESeq2 Multi-factor design not full rank
RNASeq
DESeq2
written 3.3 years ago by
jehimi
• 0
0
votes
4
replies
243
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor
clusterProfiler
updated 3 days ago by
James W. MacDonald
67k • written 5 days ago by
semra
• 0
0
votes
0
replies
103
views
Job:
Postdoctoral Research Associate in Computational Epigenomics
Phd
SingleCell
DNAMethylation
Shanghai
JobPosting
7 days ago
xiaolong
• 0
0
votes
1
reply
155
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 7 days ago by
Vincent J. Carey, Jr.
6.7k • written 7 days ago by
kmzhou4
• 0
0
votes
0
replies
124
views
News:
Bioconductor 3.20 Release Schedule
software
release
Release
7 days ago
shepherl
4.0k
1
vote
1
reply
245
views
Help with design matrix for RNA-seq data using edgeR
edgeR
RNASeqData
updated 7 days ago by
Gordon Smyth
51k • written 9 days ago by
erik.burchard
• 0
3
votes
6
replies
1.2k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 5 days ago by
Michael Love
42k • written 8 days ago by
micolak0115
• 0
0
votes
2
replies
244
views
tximport data import
tximport
updated 8 days ago by
Michael Love
42k • written 9 days ago by
rodongo
• 0
2
votes
1
reply
173
views
Should tSNE from biol. replicates look alike?
scRNAseq
SingleCellExperiment
batchelor
updated 8 days ago by
James W. MacDonald
67k • written 8 days ago by
Jose Guillen
▴ 10
0
votes
0
replies
110
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets
differential-abundance
8 days ago
샤니쿠마리
• 0
2
votes
2
replies
456
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
9 days ago • updated 8 days ago
Assa Yeroslaviz
★ 1.5k
1
vote
1
reply
228
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
updated 9 days ago by
Guido Hooiveld
★ 4.1k • written 10 days ago by
b8177
• 0
0
votes
0
replies
127
views
News:
Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
Conference
Bioconductor
Community
10 days ago
Maria Doyle
▴ 90
0
votes
1
reply
157
views
Unable to install/use limma
limma
Bioconductor
updated 10 days ago by
James W. MacDonald
67k • written 10 days ago by
Jennifer
• 0
1
vote
3
replies
562
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 10 days ago by
James W. MacDonald
67k • written 7 months ago by
Pez
▴ 10
1
vote
1
reply
222
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray
ChAMP
R
updated 10 days ago by
James W. MacDonald
67k • written 12 days ago by
Fateme
• 0
0
votes
1
reply
172
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion
ReactomeGSA
BatchEffect
updated 8 days ago by
jg
▴ 20 • written 11 days ago by
Shaimaa Gamal
• 0
3
votes
6
replies
25k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.0 years ago by
183227851
• 0
0
votes
1
reply
281
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 11 days ago by
Guido Hooiveld
★ 4.1k • written 13 days ago by
sherinesaber
• 0
0
votes
0
replies
205
views
Z-score Interpretation across components
MAST
14 days ago
Greg
• 0
0
votes
1
reply
228
views
error for the geneGOEnricher function of the NoRCE package
NoRCE
updated 14 days ago by
James W. MacDonald
67k • written 14 days ago by
Luca
• 0
0
votes
2
replies
659
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq
DESeq2
updated 14 days ago by
swbarnes2
★ 1.4k • written 15 days ago by
Shwetal
• 0
1
vote
2
replies
246
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN
biomaRt
14 days ago • updated 11 days ago
varga.luca
• 0
1
vote
5
replies
533
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler
heatmaps
written 26 days ago by
Claudio
• 0
1
vote
2
replies
235
views
Review process for delivering R packages
Bioconductor
15 days ago
XFWu
• 0
4
votes
11
replies
563
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
16 days ago • updated 14 days ago
boczniak767
▴ 740
0
votes
2
replies
279
views
Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray
sesameData
sesame
16 days ago
ramiro.barrantes
▴ 10
0
votes
2
replies
235
views
DiffBind for MBD-seq
MBD-seq
DiffBind
16 days ago
Marianna
▴ 20
0
votes
0
replies
145
views
Job:
Ensembl Job Vacancies
genomes
Annotation
GenomicVariation
ensembldb
16 days ago
Aleena
▴ 30
2
votes
9
replies
573
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR
variancePartition
updated 15 days ago by
Gordon Smyth
51k • written 17 days ago by
Seymoo
• 0
0
votes
1
reply
216
views
News:
BioCAsia 2024 Registration Now Open!
BioCAsia2024
Conference
Community
Bioconductor
17 days ago • updated 16 days ago
Maria Doyle
▴ 90
1
vote
2
replies
217
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2
RNASeqData
apeglm
17 days ago
Gordon
• 0
46,003 results • Page
1 of 921
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Comment: When doing differential methylation using the sesame package, seems to only go
by
ramiro.barrantes
▴ 10
Hello, Thank you. I absolutely respect what you mention about p-values and logFC, I was just going to tackle that soon and thank you for po…
Comment: QSEA:Error in h(simpleError(msg, call))
by
kf
• 0
genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
by
James W. MacDonald
67k
I don't know what you mean by 'a pairwise comparison', but the two analyses are equivalent, except in the second analysis you want to do `t…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
by
James W. MacDonald
67k
If you want to comment on an answer, please choose ADD COMMENT rather than ADD ANSWER, since you are not in fact adding an answer. ``` uni…
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
by
Fatima
• 0
In fact, I used the BP ontology and I am using gene symbols rather than identifiers (IDs). Is there a way to verify how many genes from the…
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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