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Input Question for deseq.r
RSeqAn
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Nina
• 0
4
votes
6
replies
445
views
FilterByExpr low counts with small sample size
edgeR
22 days ago • updated 17 days ago
Jonathan
▴ 10
0
votes
4
replies
246
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
22 days ago • updated 20 days ago
lonn
• 0
1
vote
2
replies
721
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
22 days ago • updated 13 days ago
ussarizona
▴ 10
0
votes
1
reply
154
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
quanah.hudson
• 0
0
votes
7
replies
326
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
23 days ago • updated 17 days ago
hortense96
• 0
0
votes
0
replies
88
views
News:
Services
flowBeads
23 days ago
creativepeptides2018
• 0
0
votes
0
replies
87
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Enzyme Engineering
BioTIP
23 days ago
bocchemistry
• 0
0
votes
0
replies
86
views
News:
TIDES USA 2024
flowBeads
23 days ago
bocsci11
• 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 21 days ago by
Michael Love
42k • written 23 days ago by
Brynn
• 0
0
votes
1
reply
161
views
Adding columns to DEXSeqResults object
DEXSeq
updated 21 days ago by
Alejandro Reyes
★ 1.9k • written 23 days ago by
Clyde
• 0
0
votes
0
replies
96
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
23 days ago
Maliha Tabassum
• 0
1
vote
2
replies
147
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
23 days ago
Ana
• 0
0
votes
1
reply
125
views
what is the sampleFiles
chipseq
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
zhulin
• 0
0
votes
4
replies
200
views
flowStats Search Error
flowStats
updated 23 days ago by
shepherl
3.9k • written 24 days ago by
tholmes
• 0
0
votes
0
replies
99
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
24 days ago
Virangika
• 0
0
votes
0
replies
76
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
24 days ago
Henry
▴ 10
0
votes
3
replies
209
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
331
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
25 days ago • updated 24 days ago
daniel.carbajo
• 0
0
votes
4
replies
277
views
DEG with low counts
DESeq2
updated 20 days ago by
Michael Love
42k • written 25 days ago by
Rajat
• 0
1
vote
2
replies
580
views
GSVA error
GSVA
26 days ago • updated 24 days ago
Alex
• 0
0
votes
1
reply
135
views
Deseq2 Rlog transformation
DESeq2
updated 24 days ago by
ATpoint
★ 4.1k • written 26 days ago by
Sahar
• 0
1
vote
1
reply
191
views
Differentially expressed genes in monocle pseudotime
monocle
updated 24 days ago by
Gordon Smyth
50k • written 26 days ago by
kthapa
• 0
0
votes
1
reply
144
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 23 days ago by
James W. MacDonald
65k • written 26 days ago by
tian.liu0720
• 0
2
votes
2
replies
175
views
[DiffBind] Obtaining normalization factors
DiffBind
27 days ago • updated 24 days ago
Henry
▴ 10
1
vote
2
replies
200
views
Design Matrix within group comparison more than two groups
DESeq2
27 days ago • updated 26 days ago
hemantcnaik
• 0
0
votes
1
reply
137
views
Bioinformatics student
Des
DESeq2
updated 27 days ago by
hemantcnaik
• 0 • written 27 days ago by
Sahar
• 0
2
votes
2
replies
203
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
27 days ago
julia_mcdonough
• 0
0
votes
0
replies
90
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
27 days ago
shepherl
3.9k
3
votes
3
replies
220
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
27 days ago • updated 22 days ago
jacques.imbert
• 0
2
votes
2
replies
178
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
27 days ago • updated 25 days ago
daniel.carbajo
• 0
0
votes
3
replies
267
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 21 days ago by
W. Evan Johnson
▴ 850 • written 28 days ago by
schlumbohm
• 0
0
votes
0
replies
98
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
28 days ago
Stevie Pederson
• 0
2
votes
2
replies
395
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
28 days ago • updated 27 days ago
Henry
▴ 10
0
votes
0
replies
105
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
28 days ago
communication
• 0
4
votes
9
replies
440
views
Memory errors using read.bismark?
dmrseq
bsseq
28 days ago • updated 2 days ago
Juan Higareda
• 0
3
votes
6
replies
285
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
29 days ago • updated 28 days ago
nhaus
▴ 30
0
votes
1
reply
149
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 24 days ago by
kamryncole1963
• 0 • written 29 days ago by
Sara
• 0
0
votes
1
reply
180
views
DESeq2 gives an error and R crashes
DESeq2
29 days ago • updated 28 days ago
Shefali
• 0
1
vote
2
replies
246
views
How to retrieve detailed regression results from deseq2
DESeq2
29 days ago • updated 20 days ago
Weiqian
▴ 10
5
votes
9
replies
938
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 21 days ago
Chris
• 0
0
votes
0
replies
141
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
29 days ago
Eryn
• 0
0
votes
0
replies
88
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
29 days ago
Dennis
• 0
0
votes
1
reply
165
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 25 days ago by
Guido Hooiveld
★ 3.9k • written 29 days ago by
Lucie
• 0
0
votes
4
replies
230
views
Storing directories inside an ExperimentHub package?
ExperimentHub
29 days ago • updated 28 days ago
Tim Barry
• 0
8
votes
23
replies
973
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 28 days ago by
Robert Castelo
★ 3.3k • written 29 days ago by
Bine
▴ 40
1
vote
3
replies
355
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 25 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Simran
• 0
0
votes
1
reply
156
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zh9118
• 0
0
votes
1
reply
173
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
Adelaide
• 0
5
votes
6
replies
436
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 27 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
nhaus
▴ 30
1,744 results • Page
3 of 35
Recent ...
Replies
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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