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Error in termSig <= adjs.cutOff when using topGO ks + elim
topGO
just now
adendekk
• 0
0
votes
1
reply
40
views
error
Biobase
3 hours ago
NATASHA
• 0
0
votes
1
reply
48
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 13 hours ago by
ATpoint
★ 4.1k • written 13 hours ago by
sajadahmad41454
• 0
1
vote
2
replies
158
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
1 day ago • updated 19 hours ago
Dylan.Sheerin
• 0
0
votes
0
replies
25
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
23 hours ago
neilzhao
▴ 30
1
vote
0
replies
266
views
News:
Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
7 weeks ago • updated 1 day ago
shepherl
3.9k
0
votes
1
reply
51
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
sajadahmad41454
• 0
3
votes
4
replies
448
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 2 days ago by
Mike Smith
★ 6.5k • written 5 days ago by
robersy
• 0
2
votes
5
replies
180
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
2 days ago • updated 17 hours ago
sajadahmad41454
• 0
0
votes
0
replies
30
views
Treeio as.treedata function seq lenght error
treeio
2 days ago
nromerov
• 0
1
vote
1
reply
122
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zzrammal
• 0
3
votes
10
replies
273
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 8 hours ago by
James W. MacDonald
65k • written 3 days ago by
Abbey
• 0
1
vote
1
reply
101
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
e1271094
• 0
0
votes
1
reply
64
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 3 days ago by
shepherl
3.9k • written 3 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
47
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
3 days ago
Dinesh
• 0
3
votes
5
replies
216
views
Help with running egsea()
EGSEA
4 days ago • updated 2 days ago
Chris
• 0
3
votes
1
reply
104
views
How to save the DEXSeq results
DEXSeq
updated 4 days ago by
Michael Love
42k • written 4 days ago by
Sara
• 0
3
votes
4
replies
226
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 2 days ago by
Gordon Smyth
50k • written 4 days ago by
Chris
• 0
0
votes
3
replies
143
views
Couldn't connect to server while using "pathways"
graphite
updated 4 days ago by
Michael Love
42k • written 4 days ago by
fduguchunhui
• 0
1
vote
1
reply
97
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 4 days ago by
Michael Love
42k • written 4 days ago by
mat149
▴ 70
1
vote
1
reply
143
views
Handling multiple differential expression comparisons
DESeq2
updated 5 days ago by
Michael Love
42k • written 7 days ago by
Zainab
▴ 10
2
votes
2
replies
182
views
fgsea significant result
fgsea
5 days ago
Chris
• 0
0
votes
40
replies
2.8k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 8 hours ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
6
replies
244
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 6 days ago by
swbarnes2
★ 1.4k • written 8 days ago by
arfranco
▴ 130
1
vote
2
replies
358
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
Kim
• 0
2
votes
3
replies
203
views
package goseq seems to be not available on the latest version of R
goseq
updated 4 days ago by
Gordon Smyth
50k • written 7 days ago by
Patrycja
▴ 20
2
votes
3
replies
206
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Reza
• 0
0
votes
0
replies
89
views
dba.plotProfile() plotting and interpretation
DiffBind
7 days ago
Henry
▴ 10
0
votes
1
reply
141
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
z_bahari
• 0
0
votes
1
reply
124
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
c53aba27
• 0
4
votes
2
replies
578
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
8 days ago • updated 4 days ago
gene_bioconductor
▴ 10
0
votes
0
replies
69
views
flowStats for CyTOF
flowStats
8 days ago
tholmes
• 0
0
votes
2
replies
128
views
DESeq2 v1.35.0
DESeq2
updated 8 days ago by
Michael Love
42k • written 8 days ago by
Espresso
• 0
0
votes
0
replies
63
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
8 days ago
yvonneh
• 0
0
votes
0
replies
60
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 days ago
Ian D.
▴ 70
0
votes
1
reply
97
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 8 days ago by
4r-rtg
• 0
0
votes
3
replies
198
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
9 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
2
replies
167
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
8 days ago • updated 7 days ago
kcarey
• 0
0
votes
3
replies
171
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
james.zhang20
• 0
1
vote
3
replies
261
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 9 days ago by
angelathuynh5
• 0
4
votes
0
replies
103
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
9 days ago
shepherl
3.9k
0
votes
0
replies
115
views
Empty table plot using plotGseaTable()
fgsea
9 days ago • updated 7 days ago
Chris
• 0
0
votes
3
replies
184
views
Store output of matchPWM()
biostrings
Biostrings
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
mat149
▴ 70
0
votes
3
replies
267
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 9 days ago by
Michael Love
42k • written 9 days ago by
HAK
• 0
1
vote
2
replies
253
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
9 days ago • updated 8 days ago
Yveto
• 0
8
votes
7
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 days ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
242
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
SSSJec
• 0
3
votes
4
replies
236
views
Help with error using camera() in limma
CAMERA
limma
10 days ago
Chris
• 0
1
vote
1
reply
133
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 10 days ago by
Michael Love
42k • written 10 days ago by
marcusn
• 0
0
votes
2
replies
145
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
10 days ago • updated 7 days ago
Aurora
• 0
1,000 results • Page
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Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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