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Votes
6
votes
5
replies
418
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
5
votes
6
replies
414
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 19 days ago by
ATpoint
★ 4.1k • written 23 days ago by
nhaus
▴ 30
0
votes
7
replies
401
views
DESeq filtering specific to contrasts
DESeq2
updated 12 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
4
votes
6
replies
398
views
FilterByExpr low counts with small sample size
edgeR
14 days ago • updated 9 days ago
Jonathan
▴ 10
2
votes
6
replies
386
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
23 days ago
Chris
• 0
4
votes
8
replies
382
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 13 days ago by
Peter Hickey
▴ 740 • written 21 days ago by
Juan Higareda
• 0
2
votes
2
replies
379
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
20 days ago • updated 19 days ago
Henry
▴ 10
1
vote
13
replies
368
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
10 days ago • updated 7 days ago
fernanda.backsouza
▴ 10
0
votes
2
replies
347
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 29 days ago
Gordon
• 0
1
vote
3
replies
342
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
2
votes
9
replies
340
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
0
votes
1
reply
333
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 22 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
0
votes
6
replies
324
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 days ago by
Tim Peters
▴ 170 • written 29 days ago by
s.malik
• 0
0
votes
8
replies
321
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
2
votes
3
replies
316
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
17 days ago • updated 16 days ago
daniel.carbajo
• 0
3
votes
3
replies
315
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 0
0
votes
4
replies
302
views
Help with design.matrix
limma
26 days ago • updated 25 days ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
298
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
3
votes
1
reply
293
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
0
votes
7
replies
288
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
15 days ago • updated 9 days ago
hortense96
• 0
0
votes
2
replies
287
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 26 days ago
fer_talavera
• 0
1
vote
7
replies
287
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
6 days ago • updated 5 days ago
pl23
• 0
0
votes
5
replies
284
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 8 days ago by
James W. MacDonald
65k • written 10 days ago by
Gayatri
• 0
3
votes
6
replies
264
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
21 days ago
nhaus
▴ 30
0
votes
4
replies
259
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 17 days ago by
Rajat
• 0
1
vote
0
replies
256
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
13 days ago • updated 12 days ago
BioinfGuru
▴ 30
0
votes
4
replies
251
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
2
replies
250
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
0
votes
3
replies
249
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 13 days ago by
W. Evan Johnson
▴ 850 • written 20 days ago by
schlumbohm
• 0
1
vote
3
replies
240
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
237
views
How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago
Weiqian
▴ 10
0
votes
4
replies
237
views
Minfi - estimatecellscount
min
minfi
updated 3 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
0
votes
2
replies
236
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
9 days ago • updated 7 days ago
shuwangxinze1996
• 0
2
votes
5
replies
236
views
get BM error
ensembldb
updated 7 days ago by
James W. MacDonald
65k • written 8 days ago by
Fara
• 0
0
votes
2
replies
233
views
Regressing out batch effects
DESeq2
updated 22 days ago by
Michael Love
41k • written 28 days ago by
kys91240
• 0
0
votes
1
reply
232
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 28 days ago by
Tim Peters
▴ 170 • written 28 days ago by
Kim
• 0
0
votes
4
replies
227
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
15 days ago • updated 12 days ago
lonn
• 0
1
vote
2
replies
224
views
MethylKit read issue
methylKit
updated 26 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
21 days ago • updated 20 days ago
Tim Barry
• 0
0
votes
2
replies
214
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 22 days ago by
Michael Love
41k • written 27 days ago by
nhaus
▴ 30
2
votes
5
replies
213
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 6 days ago by
James W. MacDonald
65k • written 8 days ago by
bandconductor
• 0
1
vote
4
replies
212
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 9 days ago by
James W. MacDonald
65k • written 13 days ago by
Mirella Aurora
• 0
3
votes
3
replies
212
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
WardDeb
• 0
0
votes
3
replies
209
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 18 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
1
vote
2
replies
206
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
14 days ago • updated 13 days ago
Le
• 0
0
votes
3
replies
202
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 1 day ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
0
votes
1
reply
201
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
1
vote
3
replies
200
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
200
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
andrebolerbarros
▴ 20
3
votes
2
replies
200
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 10 days ago by
Guido Hooiveld
★ 3.9k • written 12 days ago by
fernanda.backsouza
▴ 10
201 results • Page
2 of 5
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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