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33
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ChAMP installation issue
Cha
ChAMP
updated 1 hour ago by
shepherl
3.9k • written 8 hours ago by
e1271094
• 0
0
votes
1
reply
47
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 4 hours ago by
Guido Hooiveld
★ 3.9k • written 20 hours ago by
aogunbaw
• 0
2
votes
2
replies
199
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
5 days ago • updated 4 hours ago
zzrammal
• 0
0
votes
0
replies
20
views
Anti-Human APCS Recombinant Antibody (Dezamizumab)
healthyFlowData
9 hours ago
Lupe
• 0
0
votes
0
replies
37
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
23 hours ago
Seungmin
• 0
0
votes
0
replies
44
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
1 day ago
Matthew Thornton
▴ 350
0
votes
4
replies
322
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 1 day ago by
Ziliang
• 0 • written 12 days ago by
Ian D.
▴ 70
0
votes
3
replies
7.7k
views
SingleR Label.Ont
SingleR
updated 2 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
2
votes
7
replies
288
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
5 days ago • updated 2 days ago
sajadahmad41454
• 0
0
votes
0
replies
47
views
The 'Home' shows:An error has occurred. Check your logs or contact the app author for clarification.
Reports
2 days ago
315005358
• 0
1
vote
5
replies
500
views
Can't post a question containing code?
Bioconductor
updated 2 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
0
votes
1
reply
80
views
error
Biobase
2 days ago
NATASHA
• 0
3
votes
10
replies
374
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
Abbey
• 0
0
votes
40
replies
2.9k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 3 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 3 days ago by
maria.soler
• 0 • written 15 months ago by
kalavattam
▴ 10
0
votes
1
reply
80
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
sajadahmad41454
• 0
5
votes
3
replies
285
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 3 days ago by
Gordon Smyth
50k • written 25 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
190
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
4 days ago • updated 3 days ago
Dylan.Sheerin
• 0
0
votes
0
replies
39
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
3 days ago
neilzhao
▴ 30
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 3 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
1
vote
0
replies
287
views
News:
Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
7 weeks ago • updated 3 days ago
shepherl
3.9k
0
votes
1
reply
71
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
sajadahmad41454
• 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 4 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
3
votes
4
replies
475
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 5 days ago by
Mike Smith
★ 6.5k • written 7 days ago by
robersy
• 0
1
vote
3
replies
276
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 11 days ago by
angelathuynh5
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 5 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
3
votes
5
replies
238
views
Help with running egsea()
EGSEA
6 days ago • updated 5 days ago
Chris
▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 5 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
0
replies
44
views
Treeio as.treedata function seq lenght error
treeio
5 days ago
nromerov
• 0
3
votes
4
replies
253
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 5 days ago by
Gordon Smyth
50k • written 7 days ago by
Chris
▴ 10
4
votes
9
replies
462
views
Memory errors using read.bismark?
dmrseq
bsseq
4 weeks ago • updated 5 days ago
Juan Higareda
• 0
2
votes
1
reply
128
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
e1271094
• 0
0
votes
1
reply
81
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 6 days ago by
shepherl
3.9k • written 6 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
62
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
6 days ago
Dinesh
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 6 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
3
replies
167
views
Couldn't connect to server while using "pathways"
graphite
updated 6 days ago by
Michael Love
42k • written 7 days ago by
fduguchunhui
• 0
4
votes
2
replies
594
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
10 days ago • updated 6 days ago
gene_bioconductor
▴ 10
3
votes
1
reply
118
views
How to save the DEXSeq results
DEXSeq
updated 6 days ago by
Michael Love
42k • written 6 days ago by
Sara
• 0
1
vote
1
reply
113
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 6 days ago by
Michael Love
42k • written 6 days ago by
mat149
▴ 70
1
vote
2
replies
199
views
Improving the design matrices vignette in RNAseq123
RNAseq123
21 days ago • updated 7 days ago
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
217
views
package goseq seems to be not available on the latest version of R
goseq
updated 7 days ago by
Gordon Smyth
50k • written 9 days ago by
Patrycja
▴ 20
8
votes
7
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 7 days ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 7 days ago
Henrik Bengtsson
★ 2.4k
2
votes
2
replies
194
views
fgsea significant result
fgsea
8 days ago • updated 7 days ago
Chris
▴ 10
1
vote
1
reply
154
views
Handling multiple differential expression comparisons
DESeq2
updated 8 days ago by
Michael Love
42k • written 9 days ago by
Zainab
▴ 10
2
votes
3
replies
219
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 8 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Reza
• 0
0
votes
6
replies
254
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 9 days ago by
swbarnes2
★ 1.4k • written 10 days ago by
arfranco
▴ 130
1
vote
2
replies
368
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
Kim
• 0
0
votes
0
replies
126
views
Empty table plot using plotGseaTable()
fgsea
11 days ago • updated 9 days ago
Chris
▴ 10
1
vote
2
replies
338
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 9 days ago
Kim
• 0
1,726 results • Page
1 of 35
Recent ...
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Comment: ChAMP installation issue
by
shepherl
3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis
by
Guido Hooiveld
★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
zzrammal
• 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ziliang
• 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont
by
Denis
• 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Votes
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: minfi latest update for EPIC V2 chip
A: AIC-like measure for DESeq2
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