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
6
replies
164
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 14 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
arfranco
▴ 130
1
vote
2
replies
296
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 19 hours ago by
Gordon Smyth
50k • written 22 hours ago by
Kim
• 0
0
votes
1
reply
56
views
package goseq seems to be not available on the latest version of R
goseq
updated 20 hours ago by
Gordon Smyth
50k • written 23 hours ago by
Patrycja
• 0
2
votes
2
replies
105
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Reza
• 0
0
votes
0
replies
37
views
Handling multiple differential expression comparisons
DESeq2
1 day ago
Zainab
• 0
0
votes
0
replies
33
views
dba.plotProfile() plotting and interpretation
DiffBind
1 day ago
Henry
▴ 10
0
votes
1
reply
85
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
z_bahari
• 0
0
votes
1
reply
80
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
c53aba27
• 0
1
vote
1
reply
177
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
gene_bioconductor
▴ 10
0
votes
0
replies
31
views
flowStats for CyTOF
flowStats
2 days ago
tholmes
• 0
0
votes
2
replies
78
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Espresso
• 0
0
votes
0
replies
38
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
2 days ago
yvonneh
• 0
0
votes
0
replies
31
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
2 days ago
Ian D.
▴ 70
0
votes
1
reply
43
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by
4r-rtg
• 0
0
votes
2
replies
111
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
2
replies
112
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago
kcarey
• 0
0
votes
3
replies
112
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
james.zhang20
• 0
0
votes
1
reply
121
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 2 days ago by
angelathuynh5
• 0
3
votes
0
replies
55
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
2 days ago
shepherl
3.9k
0
votes
0
replies
72
views
Empty table plot using plotGseaTable()
fgsea
3 days ago • updated 22 hours ago
Chris
• 0
0
votes
3
replies
139
views
Store output of matchPWM()
biostrings
Biostrings
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
mat149
▴ 70
0
votes
3
replies
233
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
HAK
• 0
0
votes
2
replies
210
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
3 days ago • updated 2 days ago
Yveto
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
215
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
SSSJec
• 0
3
votes
4
replies
191
views
Help with error using camera() in limma
CAMERA
limma
4 days ago
Chris
• 0
1
vote
1
reply
94
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
marcusn
• 0
0
votes
2
replies
109
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
4 days ago • updated 1 day ago
Aurora
• 0
0
votes
1
reply
93
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
Agung
• 0
0
votes
0
replies
54
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
4 days ago
Maria Doyle
▴ 70
0
votes
1
reply
72
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 4 days ago by
shepherl
3.9k • written 4 days ago by
bounlu
• 0
0
votes
1
reply
94
views
putting my own expression data in deseq2
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Dev
• 0
2
votes
2
replies
178
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
5 days ago • updated 4 days ago
Chris
• 0
0
votes
3
replies
225
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
SSSJec
• 0
0
votes
0
replies
64
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
5 days ago
Chris
• 0
3
votes
3
replies
208
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
bioinf
▴ 10
1
vote
1
reply
114
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 7 days ago by
Leo Lahti
▴ 40 • written 8 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
193
views
PCA plot suggestions
DESeq2
PCAtools
updated 8 days ago by
Michael Love
41k • written 9 days ago by
Aaliya
• 0
1
vote
3
replies
204
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 8 days ago by
Michael Love
41k • written 9 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
127
views
ATACseq merge peaks
DiffBind
updated 8 days ago by
ATpoint
★ 4.1k • written 10 days ago by
Shloka
• 0
1
vote
1
reply
161
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 8 days ago by
Gordon Smyth
50k • written 12 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
307
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
9 days ago • updated 8 days ago
pl23
• 0
2
votes
9
replies
363
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
Alexandre
• 0
0
votes
0
replies
109
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
9 days ago • updated 1 day ago
glaciya2018
• 0
1
vote
2
replies
152
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
10 days ago • updated 9 days ago
ATpoint
★ 4.1k
0
votes
1
reply
143
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 9 days ago by
Michael Love
41k • written 10 days ago by
kcarey
• 0
0
votes
0
replies
79
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
10 days ago • updated 5 days ago
Sara
• 0
2
votes
5
replies
253
views
get BM error
ensembldb
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Fara
• 0
2
votes
5
replies
229
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
bandconductor
• 0
0
votes
0
replies
79
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 days ago
Dario Strbenac
★ 1.5k
45,616 results • Page
1 of 913
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
• 0
Popular Question
to
Theo
▴ 10
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Locations
• All
United States,
16 minutes ago
United States,
28 minutes ago
United States,
50 minutes ago
France,
50 minutes ago
United States,
1 hour ago
Traffic: 559 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