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Rank
Views
Votes
1
vote
7
replies
359
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
23 days ago • updated 22 days ago
pl23
• 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 10 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
1
reply
110
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 11 days ago by
shepherl
3.9k • written 11 days ago by
cyril.dalmasso
• 0
3
votes
10
replies
451
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 8 days ago by
James W. MacDonald
65k • written 11 days ago by
Abbey
• 0
5
votes
3
replies
307
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 8 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
2
votes
1
reply
170
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
e1271094
• 0
4
votes
2
replies
624
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
16 days ago • updated 12 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
137
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Dev
• 0
0
votes
3
replies
108
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 3 days ago by
Michael Love
42k • written 4 days ago by
Kasper
• 0
0
votes
2
replies
169
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
18 days ago • updated 15 days ago
Aurora
• 0
1
vote
2
replies
742
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 22 days ago
Patadù
▴ 10
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 26 days ago by
James W. MacDonald
65k • written 29 days ago by
John
• 0
0
votes
7
replies
363
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 25 days ago
hortense96
• 0
0
votes
1
reply
262
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
SSSJec
• 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 3 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
0
votes
2
replies
211
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
17 days ago • updated 16 days ago
kcarey
• 0
1
vote
4
replies
229
views
minfi::read.metharray.exp
minfiData
minfi
updated 24 days ago by
Basti
▴ 780 • written 26 days ago by
clacarion
• 0
0
votes
4
replies
373
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by
Ziliang
• 0 • written 17 days ago by
Ian D.
▴ 70
3
votes
2
replies
231
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 26 days ago by
Guido Hooiveld
★ 4.0k • written 29 days ago by
fernanda.backsouza
▴ 10
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 25 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
i.sudbery
▴ 40
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 10 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
2
votes
2
replies
235
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
19 days ago
Chris
▴ 10
0
votes
1
reply
155
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
c53aba27
• 0
2
votes
1
reply
142
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 12 days ago by
Michael Love
42k • written 12 days ago by
mat149
▴ 70
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 25 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
0
votes
2
replies
751
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 3 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
3
votes
4
replies
261
views
Help with error using camera() in limma
CAMERA
limma
18 days ago
Chris
▴ 10
0
votes
3
replies
223
views
Couldn't connect to server while using "pathways"
graphite
updated 12 days ago by
Michael Love
42k • written 12 days ago by
fduguchunhui
• 0
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 18 days ago by
shepherl
3.9k • written 18 days ago by
bounlu
• 0
0
votes
2
replies
106
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
2 days ago
makala
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 12 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
1
reply
139
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 days ago by
Michael Love
42k • written 19 days ago by
Agung
• 0
3
votes
5
replies
291
views
Help with running egsea()
EGSEA
12 days ago • updated 10 days ago
Chris
▴ 10
4
votes
9
replies
247
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
pangtaihin
• 0
1
vote
1
reply
189
views
Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by
Michael Love
42k • written 15 days ago by
Zainab
▴ 10
0
votes
4
replies
264
views
Minfi - estimatecellscount
min
minfi
updated 19 days ago by
James W. MacDonald
65k • written 7 weeks ago by
clacarion
• 0
2
votes
5
replies
794
views
DESeq2 setting significant p-value
DESeq2
updated 29 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
0
votes
2
replies
819
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
7
replies
449
views
DESeq filtering specific to contrasts
DESeq2
updated 29 days ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
0
votes
2
replies
929
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
0
votes
2
replies
239
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
29 days ago • updated 26 days ago
catv
• 0
2
votes
3
replies
119
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
Guillermo
• 0
1
vote
3
replies
304
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 days ago by
ATpoint
★ 4.1k • written 17 days ago by
angelathuynh5
• 0
1
vote
5
replies
515
views
Can't post a question containing code?
Bioconductor
updated 8 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 16 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
1
vote
1
reply
132
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
948
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 3 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
4
votes
6
replies
469
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 26 days ago
Jonathan
▴ 10
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 26 days ago by
taur.vil
• 0
177 results • Page
2 of 4
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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