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
7
replies
758
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 27 days ago
shepherl
3.9k
7
votes
6
replies
629
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 15 days ago by
robersy
• 0
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 3 days ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 6 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
4
votes
9
replies
495
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 13 days ago
Juan Higareda
• 0
4
votes
5
replies
339
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
15 days ago • updated 5 days ago
Chris
▴ 10
0
votes
6
replies
306
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 16 days ago by
swbarnes2
★ 1.4k • written 18 days ago by
arfranco
▴ 130
1
vote
2
replies
90
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 11 hours ago
Anna
• 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
Espresso
• 0
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 20 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 15 days ago
Henrik Bengtsson
★ 2.4k
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 28 days ago
shepherl
3.9k
3
votes
3
replies
370
views
permutation test in edgeR
rna-seq
edgeR
updated 29 days ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
2
votes
4
replies
291
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 28 days ago by
James W. MacDonald
65k • written 4 weeks ago by
Mirella Aurora
• 0
3
votes
4
replies
293
views
Store output of matchPWM()
biostrings
Biostrings
19 days ago • updated 7 days ago
mat149
▴ 70
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 20 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 3 days ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago
Chris
▴ 10
0
votes
3
replies
9.3k
views
SingleR Label.Ont
SingleR
updated 9 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
2
replies
145
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 6 days ago by
zhouwanding
▴ 10 • written 8 days ago by
Seungmin
• 0
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 17 days ago by
Gordon Smyth
50k • written 17 days ago by
Kim
• 0
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 7 days ago by
bandconductor
• 0 • written 3.6 years ago by
ZheFrench
▴ 60
1
vote
2
replies
109
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
5 days ago
Patadù
▴ 10
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
25 days ago • updated 24 days ago
pl23
• 0
5
votes
3
replies
319
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 10 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 12 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
0
votes
8
replies
522
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 6 days ago by
BioinfGuru
▴ 30 • written 7 days ago by
Eric Katagirya
• 0
2
votes
1
reply
148
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 14 days ago by
Michael Love
42k • written 14 days ago by
mat149
▴ 70
0
votes
7
replies
368
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 27 days ago
hortense96
• 0
3
votes
1
reply
329
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 26 days ago by
Michael Love
42k • written 27 days ago by
i.sudbery
▴ 40
4
votes
2
replies
635
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
18 days ago • updated 14 days ago
gene_bioconductor
▴ 10
1
vote
2
replies
138
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
6 days ago • updated 5 days ago
Daniel
• 0
0
votes
1
reply
185
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
2
votes
9
replies
428
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
Alexandre
• 0
0
votes
5
replies
325
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 26 days ago by
James W. MacDonald
65k • written 29 days ago by
Gayatri
• 0
0
votes
2
replies
171
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
20 days ago • updated 17 days ago
Aurora
• 0
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 21 days ago by
ATpoint
★ 4.1k • written 21 days ago by
bioinf
▴ 10
0
votes
4
replies
143
views
error running enricher from clusterprofiler
clusterProfiler
cluster
5 days ago
Yael
• 0
3
votes
5
replies
305
views
Help with running egsea()
EGSEA
14 days ago • updated 12 days ago
Chris
▴ 10
0
votes
1
reply
115
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 11 days ago by
ATpoint
★ 4.1k • written 11 days ago by
sajadahmad41454
• 0
1
vote
3
replies
238
views
Different Shrunk Log2FC according with reference
DESeq2
updated 26 days ago by
Michael Love
42k • written 26 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
234
views
minfi::read.metharray.exp
minfiData
minfi
updated 26 days ago by
Basti
▴ 780 • written 28 days ago by
clacarion
• 0
0
votes
2
replies
216
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago
kcarey
• 0
0
votes
4
replies
379
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 9 days ago by
Ziliang
• 0 • written 19 days ago by
Ian D.
▴ 70
0
votes
3
replies
131
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 5 days ago by
Michael Love
42k • written 6 days ago by
Kasper
• 0
2
votes
2
replies
239
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago
Chris
▴ 10
3
votes
10
replies
490
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
Abbey
• 0
1
vote
2
replies
177
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
26 days ago • updated 25 days ago
ATpoint
★ 4.1k
172 results • Page
1 of 4
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards
• All
Popular Question
to
landenshanie
▴ 40
Popular Question
to
minardsmitha
▴ 10
Teacher
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Mike
• -60
Popular Question
to
shepherl
3.9k
Locations
• All
United States,
38 minutes ago
Melbourne, Australia,
1 hour ago
France,
1 hour ago
United States,
1 hour ago
United States,
1 hour ago
Traffic: 547 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