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4
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166
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
12 days ago
sropri
• 0
1
vote
4
replies
193
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 8 days ago by
James W. MacDonald
65k • written 12 days ago by
Mirella Aurora
• 0
0
votes
3
replies
161
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 11 days ago by
Gordon Smyth
50k • written 12 days ago by
prity6459
• 0
0
votes
0
replies
105
views
Warning while loading DEP package
DEP
updated 12 days ago by
shepherl
3.8k • written 12 days ago by
Namrata
• 0
0
votes
3
replies
142
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 hours ago by
Alejandro Reyes
★ 1.9k • written 12 days ago by
Alessia
• 0
0
votes
1
reply
113
views
rlog transformation
DESeq2
updated 12 days ago by
Michael Love
41k • written 12 days ago by
ishij9717
• 0
0
votes
1
reply
96
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 12 days ago by
Michael Love
41k • written 12 days ago by
09191919
• 0
3
votes
1
reply
150
views
Log-cpm values from limma
limma
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updated 11 days ago by
Gordon Smyth
50k • written 12 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
197
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
12 days ago
Le
• 0
1
vote
2
replies
141
views
Error in champ.load(): The following specified files do not exist
ChAMP
13 days ago • updated 12 days ago
Sherin
• 0
0
votes
1
reply
89
views
Input Question for deseq.r
RSeqAn
updated 12 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Nina
• 0
4
votes
6
replies
383
views
FilterByExpr low counts with small sample size
edgeR
13 days ago • updated 8 days ago
Jonathan
▴ 10
0
votes
4
replies
214
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
13 days ago • updated 10 days ago
lonn
• 0
1
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2
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684
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
13 days ago • updated 4 days ago
ussarizona
▴ 10
0
votes
1
reply
132
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 13 days ago by
quanah.hudson
• 0
0
votes
7
replies
282
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
13 days ago • updated 7 days ago
hortense96
• 0
0
votes
0
replies
68
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13 days ago
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0
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1
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118
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covariate with negative and positive values
DESeq2
updated 12 days ago by
Michael Love
41k • written 14 days ago by
Brynn
• 0
0
votes
1
reply
139
views
Adding columns to DEXSeqResults object
DEXSeq
updated 12 days ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Clyde
• 0
0
votes
0
replies
84
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
14 days ago
Maliha Tabassum
• 0
1
vote
2
replies
125
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
14 days ago
Ana
• 0
0
votes
1
reply
109
views
what is the sampleFiles
chipseq
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
zhulin
• 0
0
votes
4
replies
171
views
flowStats Search Error
flowStats
updated 14 days ago by
shepherl
3.8k • written 15 days ago by
tholmes
• 0
0
votes
0
replies
84
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Diffbind Error in socketConnection
DiffBind
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SpikeIn
15 days ago
Virangika
• 0
0
votes
0
replies
62
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
15 days ago
Henry
▴ 10
0
votes
3
replies
189
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 14 days ago by
Michael Love
41k • written 15 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
307
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
15 days ago • updated 14 days ago
daniel.carbajo
• 0
0
votes
4
replies
246
views
DEG with low counts
DESeq2
updated 11 days ago by
Michael Love
41k • written 16 days ago by
Rajat
• 0
1
vote
2
replies
453
views
GSVA error
GSVA
16 days ago • updated 15 days ago
Alex
• 0
0
votes
1
reply
119
views
Deseq2 Rlog transformation
DESeq2
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
Sahar
• 0
1
vote
1
reply
174
views
Differentially expressed genes in monocle pseudotime
monocle
updated 14 days ago by
Gordon Smyth
50k • written 16 days ago by
kthapa
• 0
0
votes
1
reply
131
views
SNP locus package for mouse?
SNPlocs
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updated 14 days ago by
James W. MacDonald
65k • written 17 days ago by
tian.liu0720
• 0
2
votes
2
replies
159
views
[DiffBind] Obtaining normalization factors
DiffBind
18 days ago • updated 14 days ago
Henry
▴ 10
1
vote
2
replies
181
views
Design Matrix within group comparison more than two groups
DESeq2
18 days ago • updated 17 days ago
hemantcnaik
• 0
0
votes
1
reply
123
views
Bioinformatics student
Des
DESeq2
updated 18 days ago by
hemantcnaik
• 0 • written 18 days ago by
Sahar
• 0
2
votes
2
replies
183
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
18 days ago
julia_mcdonough
• 0
0
votes
0
replies
77
views
News:
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Release
release
Bioconductor
Bioconducto
18 days ago
shepherl
3.8k
3
votes
3
replies
183
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
18 days ago • updated 12 days ago
jacques.imbert
• 0
2
votes
2
replies
161
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
18 days ago • updated 15 days ago
daniel.carbajo
• 0
0
votes
3
replies
239
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 12 days ago by
W. Evan Johnson
▴ 850 • written 18 days ago by
schlumbohm
• 0
0
votes
0
replies
84
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
18 days ago
Stevie Pederson
• 0
2
votes
2
replies
374
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
19 days ago • updated 18 days ago
Henry
▴ 10
0
votes
0
replies
91
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
19 days ago
communication
• 0
4
votes
8
replies
377
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 11 days ago by
Peter Hickey
▴ 740 • written 19 days ago by
Juan Higareda
• 0
3
votes
6
replies
257
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
19 days ago
nhaus
▴ 30
0
votes
1
reply
132
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 14 days ago by
kamryncole1963
• 0 • written 19 days ago by
Sara
• 0
0
votes
1
reply
164
views
DESeq2 gives an error and R crashes
DESeq2
20 days ago • updated 19 days ago
Shefali
• 0
1
vote
2
replies
232
views
How to retrieve detailed regression results from deseq2
DESeq2
20 days ago • updated 11 days ago
Weiqian
▴ 10
1,000 results • Page
2 of 20
Recent ...
Replies
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma
by
James W. MacDonald
65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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