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
3
replies
49
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
3 hours ago
arfranco
▴ 130
0
votes
1
reply
75
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated just now by
Gordon Smyth
50k • written 5 hours ago by
gene_bioconductor
▴ 10
0
votes
1
reply
22
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 1 hour ago by
Gordon Smyth
50k • written 5 hours ago by
z_bahari
• 0
0
votes
1
reply
24
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 1 hour ago by
Gordon Smyth
50k • written 5 hours ago by
c53aba27
• 0
0
votes
0
replies
12
views
flowStats for CyTOF
flowStats
7 hours ago
tholmes
• 0
0
votes
2
replies
48
views
DESeq2 v1.35.0
DESeq2
updated 7 hours ago by
Michael Love
41k • written 8 hours ago by
Espresso
• 0
0
votes
0
replies
16
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
9 hours ago • updated 8 hours ago
yvonneh
• 0
0
votes
0
replies
15
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
9 hours ago
Ian D.
▴ 70
0
votes
1
reply
29
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 14 hours ago by
4r-rtg
• 0
0
votes
2
replies
59
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 1 hour ago
kcarey
• 0
0
votes
3
replies
93
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 13 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 0
0
votes
1
reply
98
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
angelathuynh5
• 0
3
votes
0
replies
40
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
1 day ago
shepherl
3.9k
0
votes
0
replies
55
views
Empty table plot using plotGseaTable()
fgsea
1 day ago
Chris
• 0
0
votes
3
replies
109
views
Store output of matchPWM()
biostrings
Biostrings
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
mat149
▴ 70
0
votes
2
replies
88
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 9 hours ago
Ian D.
▴ 70
0
votes
2
replies
192
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 day ago • updated 23 hours ago
Yveto
• 0
0
votes
3
replies
217
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
HAK
• 0
3
votes
4
replies
166
views
Help with error using camera() in limma
CAMERA
limma
2 days ago
Chris
• 0
1
vote
1
reply
81
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
marcusn
• 0
0
votes
0
replies
45
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
2 days ago
Maria Doyle
▴ 70
0
votes
1
reply
85
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 0
0
votes
1
reply
75
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Aurora
• 0
0
votes
1
reply
63
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 days ago by
shepherl
3.9k • written 2 days ago by
bounlu
• 0
0
votes
1
reply
204
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
0
votes
1
reply
86
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
Agung
• 0
2
votes
2
replies
168
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
3 days ago
Chris
• 0
0
votes
0
replies
55
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
0
votes
3
replies
208
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
3
votes
3
replies
197
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
1
vote
1
reply
108
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by
Leo Lahti
▴ 40 • written 6 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
187
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 6 days ago by
Michael Love
41k • written 7 days ago by
JalapenoCornbread
• 0
1
vote
7
replies
294
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago
pl23
• 0
0
votes
2
replies
182
views
PCA plot suggestions
DESeq2
PCAtools
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
0
votes
1
reply
114
views
ATACseq merge peaks
DiffBind
updated 6 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Shloka
• 0
0
votes
0
replies
72
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
8 days ago • updated 3 days ago
Sara
• 0
1
vote
4
replies
301
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
0
votes
2
replies
150
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 10 days ago by
taur.vil
• 0
1
vote
1
reply
151
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago
Chris
• 0
0
votes
3
replies
155
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Alessia
• 0
1
vote
2
replies
694
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago
ussarizona
▴ 10
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
0
votes
4
replies
237
views
Minfi - estimatecellscount
min
minfi
updated 3 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
1
vote
4
replies
456
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 7 hours ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 2 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 2 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards
• All
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Popular Question
to
shepherl
3.9k
Popular Question
to
siajunren
• 0
Scholar
to
Rory Stark
★ 5.2k
Locations
• All
WEHI, Melbourne, Australia,
2 minutes ago
France,
14 minutes ago
St Louis, MO,
25 minutes ago
United States,
1 hour ago
United States,
2 hours ago
Traffic: 629 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