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7
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323
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Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
20 days ago • updated 14 days ago
hortense96
• 0
0
votes
0
replies
84
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News:
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20 days ago
creativepeptides2018
• 0
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0
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BioTIP
20 days ago
bocchemistry
• 0
0
votes
0
replies
84
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News:
TIDES USA 2024
flowBeads
20 days ago
bocsci11
• 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 19 days ago by
Michael Love
42k • written 20 days ago by
Brynn
• 0
0
votes
1
reply
157
views
Adding columns to DEXSeqResults object
DEXSeq
updated 19 days ago by
Alejandro Reyes
★ 1.9k • written 21 days ago by
Clyde
• 0
0
votes
0
replies
94
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
21 days ago
Maliha Tabassum
• 0
1
vote
2
replies
142
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
21 days ago
Ana
• 0
0
votes
1
reply
123
views
what is the sampleFiles
chipseq
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
zhulin
• 0
0
votes
4
replies
195
views
flowStats Search Error
flowStats
updated 21 days ago by
shepherl
3.9k • written 21 days ago by
tholmes
• 0
0
votes
0
replies
96
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
22 days ago
Virangika
• 0
0
votes
0
replies
73
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
22 days ago
Henry
▴ 10
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 21 days ago by
Michael Love
42k • written 22 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
329
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
22 days ago • updated 21 days ago
daniel.carbajo
• 0
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 18 days ago by
Michael Love
42k • written 23 days ago by
Rajat
• 0
1
vote
2
replies
541
views
GSVA error
GSVA
23 days ago • updated 22 days ago
Alex
• 0
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Sahar
• 0
1
vote
1
reply
187
views
Differentially expressed genes in monocle pseudotime
monocle
updated 21 days ago by
Gordon Smyth
50k • written 23 days ago by
kthapa
• 0
0
votes
1
reply
143
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 21 days ago by
James W. MacDonald
65k • written 24 days ago by
tian.liu0720
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
25 days ago • updated 21 days ago
Henry
▴ 10
1
vote
2
replies
199
views
Design Matrix within group comparison more than two groups
DESeq2
25 days ago • updated 24 days ago
hemantcnaik
• 0
0
votes
1
reply
137
views
Bioinformatics student
Des
DESeq2
updated 25 days ago by
hemantcnaik
• 0 • written 25 days ago by
Sahar
• 0
2
votes
2
replies
198
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
25 days ago • updated 24 days ago
julia_mcdonough
• 0
0
votes
0
replies
86
views
News:
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Release
release
Bioconductor
Bioconducto
25 days ago
shepherl
3.9k
3
votes
3
replies
213
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
25 days ago • updated 19 days ago
jacques.imbert
• 0
2
votes
2
replies
175
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
25 days ago • updated 22 days ago
daniel.carbajo
• 0
0
votes
3
replies
259
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 19 days ago by
W. Evan Johnson
▴ 850 • written 25 days ago by
schlumbohm
• 0
0
votes
0
replies
94
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
25 days ago
Stevie Pederson
• 0
2
votes
2
replies
392
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
26 days ago • updated 25 days ago
Henry
▴ 10
0
votes
0
replies
101
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
26 days ago
communication
• 0
4
votes
9
replies
428
views
Memory errors using read.bismark?
dmrseq
bsseq
26 days ago • updated 5 hours ago
Juan Higareda
• 0
3
votes
6
replies
279
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
26 days ago
nhaus
▴ 30
0
votes
1
reply
145
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 21 days ago by
kamryncole1963
• 0 • written 26 days ago by
Sara
• 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
26 days ago • updated 25 days ago
Shefali
• 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
26 days ago • updated 18 days ago
Weiqian
▴ 10
5
votes
9
replies
932
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
26 days ago • updated 19 days ago
Chris
• 0
0
votes
0
replies
135
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
27 days ago
Eryn
• 0
0
votes
0
replies
87
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
27 days ago
Dennis
• 0
0
votes
1
reply
162
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 23 days ago by
Guido Hooiveld
★ 3.9k • written 27 days ago by
Lucie
• 0
0
votes
4
replies
229
views
Storing directories inside an ExperimentHub package?
ExperimentHub
27 days ago • updated 26 days ago
Tim Barry
• 0
8
votes
23
replies
956
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 26 days ago by
Robert Castelo
★ 3.3k • written 27 days ago by
Bine
▴ 40
1
vote
3
replies
352
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 22 days ago by
Gordon Smyth
50k • written 27 days ago by
Simran
• 0
0
votes
1
reply
152
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
zh9118
• 0
0
votes
1
reply
167
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 27 days ago by
Michael Love
42k • written 28 days ago by
Adelaide
• 0
5
votes
6
replies
431
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 24 days ago by
ATpoint
★ 4.1k • written 28 days ago by
nhaus
▴ 30
0
votes
0
replies
112
views
ggtree tip label position (depth)
ggtree
28 days ago • updated 27 days ago
Roope
• 0
1
vote
6
replies
495
views
GSVA on separate healthy and disease datasets
GSVA
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
Lucy
▴ 60
2
votes
6
replies
406
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
29 days ago
Chris
• 0
0
votes
1
reply
141
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 27 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Merav
• 0
0
votes
0
replies
149
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
29 days ago
arne.sahm
• 0
201 results • Page
3 of 5
Recent ...
Replies
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark?
by
Juan Higareda
• 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance
by
James W. MacDonald
65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip
by
James W. MacDonald
65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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