Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
0
votes
0
replies
14
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
2 hours ago • updated just now
Chris
• 0
0
votes
0
replies
18
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
7 hours ago
robersy
• 0
1
vote
1
reply
69
views
Handling multiple differential expression comparisons
DESeq2
updated 15 hours ago by
Michael Love
41k • written 2 days ago by
Zainab
▴ 10
2
votes
2
replies
74
views
fgsea significant result
fgsea
1 day ago • updated 8 hours ago
Chris
• 0
0
votes
29
replies
2.4k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 5 hours ago by
Michael Love
41k • written 15 months ago by
Poonam
• 0
0
votes
6
replies
190
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 day ago by
swbarnes2
★ 1.3k • written 3 days ago by
arfranco
▴ 130
1
vote
2
replies
320
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
Kim
• 0
2
votes
3
replies
101
views
package goseq seems to be not available on the latest version of R
goseq
updated 3 hours ago by
Gordon Smyth
50k • written 2 days ago by
Patrycja
▴ 20
2
votes
3
replies
151
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 17 hours ago by
ATpoint
★ 4.1k • written 2 days ago by
Reza
• 0
0
votes
0
replies
47
views
dba.plotProfile() plotting and interpretation
DiffBind
2 days ago
Henry
▴ 10
0
votes
1
reply
97
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
z_bahari
• 0
0
votes
1
reply
93
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
c53aba27
• 0
3
votes
4
replies
431
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 3 hours ago by
Chris
• 0 • written 3 days ago by
gene_bioconductor
▴ 10
0
votes
0
replies
42
views
flowStats for CyTOF
flowStats
3 days ago
tholmes
• 0
0
votes
2
replies
94
views
DESeq2 v1.35.0
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
Espresso
• 0
0
votes
0
replies
44
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
3 days ago
yvonneh
• 0
0
votes
0
replies
39
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
3 days ago
Ian D.
▴ 70
0
votes
1
reply
57
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 3 days ago by
4r-rtg
• 0
0
votes
2
replies
124
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
4 days ago • updated 3 days ago
Ian D.
▴ 70
0
votes
2
replies
127
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago
kcarey
• 0
0
votes
3
replies
131
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
james.zhang20
• 0
0
votes
1
reply
132
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
angelathuynh5
• 0
3
votes
0
replies
66
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
4 days ago
shepherl
3.9k
0
votes
0
replies
84
views
Empty table plot using plotGseaTable()
fgsea
4 days ago • updated 2 days ago
Chris
• 0
0
votes
3
replies
149
views
Store output of matchPWM()
biostrings
Biostrings
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
mat149
▴ 70
0
votes
3
replies
243
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
HAK
• 0
0
votes
2
replies
220
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 14 hours ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
223
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
SSSJec
• 0
3
votes
4
replies
199
views
Help with error using camera() in limma
CAMERA
limma
5 days ago
Chris
• 0
1
vote
1
reply
104
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 5 days ago by
Michael Love
41k • written 5 days ago by
marcusn
• 0
0
votes
2
replies
119
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
5 days ago • updated 2 days ago
Aurora
• 0
0
votes
1
reply
100
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Agung
• 0
0
votes
0
replies
59
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
5 days ago
Maria Doyle
▴ 70
0
votes
1
reply
81
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 5 days ago by
shepherl
3.9k • written 5 days ago by
bounlu
• 0
0
votes
1
reply
101
views
putting my own expression data in deseq2
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
Dev
• 0
2
votes
2
replies
189
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
6 days ago
Chris
• 0
0
votes
3
replies
235
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
SSSJec
• 0
0
votes
0
replies
70
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
6 days ago
Chris
• 0
3
votes
3
replies
223
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
bioinf
▴ 10
1
vote
1
reply
123
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 9 days ago by
Leo Lahti
▴ 40 • written 9 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
205
views
PCA plot suggestions
DESeq2
PCAtools
updated 9 days ago by
Michael Love
41k • written 11 days ago by
Aaliya
• 0
1
vote
3
replies
214
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 9 days ago by
Michael Love
41k • written 10 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
132
views
ATACseq merge peaks
DiffBind
updated 9 days ago by
ATpoint
★ 4.1k • written 11 days ago by
Shloka
• 0
1
vote
1
reply
168
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 9 days ago by
Gordon Smyth
50k • written 13 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
325
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
10 days ago • updated 9 days ago
pl23
• 0
2
votes
9
replies
388
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Alexandre
• 0
0
votes
0
replies
123
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
10 days ago • updated 2 days ago
glaciya2018
• 0
1
vote
2
replies
157
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
11 days ago • updated 10 days ago
ATpoint
★ 4.1k
0
votes
1
reply
153
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 11 days ago by
Michael Love
41k • written 11 days ago by
kcarey
• 0
45,619 results • Page
1 of 913
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
Awards
• All
Scholar
to
ATpoint
★ 4.1k
Popular Question
to
Ben
▴ 50
Popular Question
to
Sam
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
▴ 10
Locations
• All
European Union,
4 minutes ago
United States,
9 minutes ago
United Kingdom,
12 minutes ago
France,
18 minutes ago
The city by the bay,
31 minutes ago
Traffic: 519 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6