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significant difference of p-values with dream() after updating VariancePartition
variancePartition
10 minutes ago
Le
• 0
0
votes
0
replies
22
views
Error in champ.load(): The following specified files do not exist
ChAMP
11 hours ago
Sherin
• 0
0
votes
0
replies
15
views
Input Question for deseq.r
RSeqAn
13 hours ago
Nina
• 0
0
votes
1
reply
53
views
FilterByExpr low counts with small sample size
edgeR
updated 5 hours ago by
Gordon Smyth
50k • written 14 hours ago by
Jonathan
▴ 10
0
votes
0
replies
16
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 hours ago
lonn
• 0
0
votes
0
replies
26
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 hours ago • updated 15 hours ago
ussarizona
• 0
0
votes
0
replies
28
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
18 hours ago
quanah.hudson
• 0
0
votes
6
replies
116
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 8 hours ago by
Gordon Smyth
50k • written 21 hours ago by
hortense96
• 0
0
votes
0
replies
21
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News:
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21 hours ago
creativepeptides2018
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0
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18
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21 hours ago
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0
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0
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25
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News:
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flowBeads
1 day ago
bocsci11
• 0
0
votes
0
replies
42
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covariate with negative and positive values
DESeq2
1 day ago
Brynn
• 0
0
votes
0
replies
30
views
Adding columns to DEXSeqResults object
DEXSeq
1 day ago
Clyde
• 0
0
votes
0
replies
38
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
1 day ago
Maliha Tabassum
• 0
1
vote
2
replies
64
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
1 day ago
Ana
• 0
0
votes
1
reply
60
views
what is the sampleFiles
chipseq
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
zhulin
• 0
0
votes
4
replies
104
views
flowStats Search Error
flowStats
updated 1 day ago by
shepherl
3.8k • written 2 days ago by
tholmes
• 0
0
votes
0
replies
46
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
2 days ago
Virangika
• 0
0
votes
0
replies
37
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
2 days ago
Henry
▴ 10
0
votes
3
replies
128
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
217
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
3 days ago • updated 2 days ago
daniel.carbajo
• 0
0
votes
3
replies
158
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago
Rajat
• 0
1
vote
2
replies
201
views
GSVA error
GSVA
3 days ago • updated 2 days ago
Alex
• 0
0
votes
1
reply
83
views
Deseq2 Rlog transformation
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Sahar
• 0
0
votes
1
reply
96
views
Differentially expressed genes in monocle pseudotime
monocle
updated 1 day ago by
Gordon Smyth
50k • written 4 days ago by
kthapa
• 0
0
votes
1
reply
81
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 1 day ago by
James W. MacDonald
65k • written 4 days ago by
tian.liu0720
• 0
2
votes
2
replies
123
views
[DiffBind] Obtaining normalization factors
DiffBind
5 days ago • updated 1 day ago
Henry
▴ 10
1
vote
2
replies
145
views
Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago
hemantcnaik
• 0
0
votes
1
reply
100
views
Bioinformatics student
Des
DESeq2
updated 5 days ago by
hemantcnaik
• 0 • written 5 days ago by
Sahar
• 0
2
votes
2
replies
135
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 days ago
julia_mcdonough
• 0
0
votes
0
replies
60
views
Cell type in SVD analysis
ChAMP
5 days ago
simleopold11
• 0
0
votes
0
replies
58
views
News:
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Release
release
Bioconductor
Bioconducto
5 days ago
shepherl
3.8k
0
votes
2
replies
100
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
updated 2 days ago by
Peter Hickey
▴ 710 • written 5 days ago by
jacques.imbert
• 0
2
votes
2
replies
124
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 days ago • updated 3 days ago
daniel.carbajo
• 0
0
votes
2
replies
134
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
5 days ago • updated 1 day ago
schlumbohm
• 0
0
votes
0
replies
65
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
6 days ago
Stevie Pederson
• 0
2
votes
2
replies
331
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
6 days ago • updated 5 days ago
Henry
▴ 10
0
votes
0
replies
69
views
News:
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sequencing
Sequencing
SequencingData
6 days ago
communication
• 0
4
votes
8
replies
272
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 7 hours ago by
Peter Hickey
▴ 710 • written 6 days ago by
Juan Higareda
• 0
3
votes
6
replies
200
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
6 days ago
nhaus
▴ 30
0
votes
1
reply
97
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 2 days ago by
kamryncole1963
• 0 • written 6 days ago by
Sara
• 0
0
votes
1
reply
138
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago
Shefali
• 0
1
vote
1
reply
153
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by
Michael Love
41k • written 7 days ago by
Weiqian
▴ 10
5
votes
9
replies
742
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
7 days ago • updated 3 hours ago
Chris
• 0
0
votes
0
replies
98
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
7 days ago
Eryn
• 0
0
votes
0
replies
65
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
7 days ago
Dennis
• 0
0
votes
1
reply
104
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 7 days ago by
Lucie
• 0
0
votes
4
replies
175
views
Storing directories inside an ExperimentHub package?
ExperimentHub
7 days ago • updated 6 days ago
Tim Barry
• 0
8
votes
23
replies
728
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 6 days ago by
Robert Castelo
★ 3.2k • written 7 days ago by
Bine
▴ 40
1
vote
3
replies
286
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 2 days ago by
Gordon Smyth
50k • written 8 days ago by
Simran
• 0
1,000 results • Page
1 of 20
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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