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
1
vote
2
replies
56
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
11 hours ago • updated just now
Chris
• 0
1
vote
2
replies
170
views
Improving the design matrices vignette in RNAseq123
RNAseq123
14 days ago • updated just now
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
135
views
package goseq seems to be not available on the latest version of R
goseq
updated 1 hour ago by
Gordon Smyth
50k • written 2 days ago by
Patrycja
▴ 20
0
votes
1
reply
27
views
Couldn't connect to server while using "pathways"
DESeq2
updated 3 hours ago by
ATpoint
★ 4.1k • written 5 hours ago by
fduguchunhui
• 0
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 hours ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
3
votes
1
reply
469
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 8 hours ago by
Gordon Smyth
50k • written 3 days ago by
gene_bioconductor
▴ 10
0
votes
29
replies
2.5k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 14 hours ago by
Michael Love
41k • written 15 months ago by
Poonam
• 0
0
votes
5
replies
2.8k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 15 hours ago
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
22
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
16 hours ago
robersy
• 0
2
votes
2
replies
98
views
fgsea significant result
fgsea
1 day ago • updated 17 hours ago
Chris
• 0
1
vote
1
reply
85
views
Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Zainab
▴ 10
2
votes
3
replies
158
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
Reza
• 0
0
votes
6
replies
200
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 2 days ago by
swbarnes2
★ 1.3k • written 3 days ago by
arfranco
▴ 130
1
vote
2
replies
325
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
0
votes
0
replies
87
views
Empty table plot using plotGseaTable()
fgsea
4 days ago • updated 2 days ago
Chris
• 0
1
vote
2
replies
296
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 2 days ago
Kim
• 0
0
votes
0
replies
48
views
dba.plotProfile() plotting and interpretation
DiffBind
2 days ago
Henry
▴ 10
0
votes
2
replies
120
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
6 days ago • updated 3 days ago
Aurora
• 0
0
votes
0
replies
124
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
11 days ago • updated 3 days ago
glaciya2018
• 0
0
votes
2
replies
130
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago
kcarey
• 0
0
votes
1
reply
102
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
97
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
c53aba27
• 0
0
votes
0
replies
43
views
flowStats for CyTOF
flowStats
3 days ago
tholmes
• 0
0
votes
2
replies
97
views
DESeq2 v1.35.0
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
Espresso
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 3 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
0
replies
45
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
3 days ago
yvonneh
• 0
0
votes
0
replies
40
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
3 days ago
Ian D.
▴ 70
0
votes
2
replies
128
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
5 days ago • updated 3 days ago
Ian D.
▴ 70
0
votes
1
reply
59
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 days ago by
4r-rtg
• 0
0
votes
3
replies
132
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
james.zhang20
• 0
0
votes
2
replies
165
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 13 days ago by
taur.vil
• 0
0
votes
2
replies
222
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
0
votes
3
replies
247
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
1
reply
135
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
68
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
4 days ago
shepherl
3.9k
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
15 days ago • updated 4 days ago
Chris
• 0
0
votes
3
replies
154
views
Store output of matchPWM()
biostrings
Biostrings
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
mat149
▴ 70
1
vote
4
replies
479
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 4 days ago
JKim
• 0
3
votes
4
replies
204
views
Help with error using camera() in limma
CAMERA
limma
5 days ago
Chris
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 5 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 5 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
225
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
0
votes
3
replies
239
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
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 5 days ago
Chris
• 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 5 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
166
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 18 days ago by
Alessia
• 0
1
vote
1
reply
106
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
marcusn
• 0
0
votes
1
reply
101
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
61
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
6 days ago
Maria Doyle
▴ 70
0
votes
1
reply
85
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 6 days ago by
shepherl
3.9k • written 6 days ago by
bounlu
• 0
54 results • Page
1 of 2
Recent ...
Replies
Comment: Method to find pathways different between 2 groups
by
Chris
• 0
Sorry for not clear. I just try to find papers use this method for learning purpose.
Comment: Improving the design matrices vignette in RNAseq123
by
Lluís Revilla Sancho
▴ 730
Cool. Thanks for looking into it.
Comment: Couldn't connect to server while using "pathways"
by
ATpoint
★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma 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 unavailability.…
Votes
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
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
Netherlands,
1 minute ago
United States,
1 minute ago
European Union,
5 minutes ago
France,
7 minutes ago
WEHI, Melbourne, Australia,
15 minutes ago
Traffic: 772 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