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
11
views
Subsetting RNAseq data | voomaByGroup()
limma
4 hours ago
Anna
• 0
0
votes
0
replies
15
views
ERROR; return code from pthread_create() is 22
affy
4 hours ago
pickingastar
• 0
0
votes
0
replies
22
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
9 hours ago • updated 5 hours ago
Abiologist
• 0
0
votes
2
replies
68
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 3 hours ago by
Michael Love
42k • written 1 day ago by
shaunpeterson
• 0
0
votes
3
replies
87
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 1 day ago by
damian.szk
▴ 80 • written 1 day ago by
ninidea
• 0
0
votes
3
replies
168
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 2 hours ago by
Michael Love
42k • written 1 day ago by
Ken C
• 0
0
votes
2
replies
103
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
2 days ago • updated 1 day ago
makala
• 0
0
votes
0
replies
46
views
determine k during RUVSeq
RUVSeq
RUVnormalize
2 days ago
Ειρήνη
• 0
0
votes
0
replies
46
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
2 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
2 days ago
oliverelijhan
0
0
votes
0
replies
62
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
2 days ago
Anton01
• 0
2
votes
3
replies
95
views
Problem installing ChAMP on a MacBook
ChAMP
updated 2 days ago by
shepherl
3.9k • written 2 days ago by
Galia
• 0
0
votes
0
replies
40
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
2 days ago
danalvoronov
▴ 10
0
votes
0
replies
35
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
2 days ago
k200987
• 0
2
votes
5
replies
210
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
3 days ago • updated 1 day ago
Patadù
▴ 10
0
votes
4
replies
124
views
error running enricher from clusterprofiler
clusterProfiler
cluster
3 days ago • updated 2 days ago
Yael
• 0
2
votes
3
replies
117
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Guillermo
• 0
0
votes
0
replies
34
views
Difference in Contrast in DiffBind
DiffBind
3 days ago
zzrammal
• 0
4
votes
9
replies
241
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
pangtaihin
• 0
1
vote
2
replies
89
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
3 days ago
Patadù
▴ 10
0
votes
3
replies
106
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 3 days ago by
Michael Love
42k • written 3 days ago by
Kasper
• 0
1
vote
2
replies
121
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
4 days ago • updated 2 days ago
Daniel
• 0
1
vote
0
replies
55
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
4 days ago
Aleena
▴ 30
0
votes
0
replies
49
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
4 days ago
Researcher
• 0
1
vote
3
replies
237
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Ashley
• 0
1
vote
2
replies
228
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
4 days ago • updated 1 day ago
BioinfGuru
▴ 30
0
votes
8
replies
489
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 3 days ago by
BioinfGuru
▴ 30 • written 4 days ago by
Eric Katagirya
• 0
0
votes
1
reply
87
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 4 days ago by
Michael Love
42k • written 5 days ago by
piemmea
• 0
0
votes
2
replies
96
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
2
votes
1
reply
67
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 3 days ago by
Alejandro Reyes
★ 1.9k • written 5 days ago by
Sara
• 0
0
votes
3
replies
173
views
ChAMP installation issue
Cha
ChAMP
5 days ago • updated 4 days ago
e1271094
• 0
0
votes
1
reply
127
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 5 days ago by
Guido Hooiveld
★ 4.0k • written 6 days ago by
aogunbaw
• 0
0
votes
2
replies
123
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 3 days ago by
zhouwanding
▴ 10 • written 6 days ago by
Seungmin
• 0
2
votes
2
replies
353
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
6 days ago • updated 2 days ago
Matthew Thornton
▴ 360
0
votes
1
reply
165
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
0
votes
0
replies
73
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
8 days ago
neilzhao
▴ 30
0
votes
1
reply
101
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
sajadahmad41454
• 0
1
vote
2
replies
261
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
9 days ago • updated 8 days ago
Dylan.Sheerin
• 0
2
votes
7
replies
374
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
10 days ago • updated 7 days ago
sajadahmad41454
• 0
0
votes
0
replies
71
views
Treeio as.treedata function seq lenght error
treeio
10 days ago
nromerov
• 0
2
votes
2
replies
274
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
11 days ago • updated 5 days ago
zzrammal
• 0
3
votes
10
replies
447
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 8 days ago by
James W. MacDonald
65k • written 11 days ago by
Abbey
• 0
0
votes
1
reply
108
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 11 days ago by
shepherl
3.9k • written 11 days ago by
cyril.dalmasso
• 0
2
votes
1
reply
168
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
e1271094
• 0
0
votes
0
replies
89
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 days ago
Dinesh
• 0
3
votes
5
replies
290
views
Help with running egsea()
EGSEA
11 days ago • updated 10 days ago
Chris
▴ 10
3
votes
1
reply
148
views
How to save the DEXSeq results
DEXSeq
updated 12 days ago by
Michael Love
42k • written 12 days ago by
Sara
• 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 12 days ago by
Michael Love
42k • written 12 days ago by
mat149
▴ 70
0
votes
3
replies
220
views
Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by
Michael Love
42k • written 12 days ago by
fduguchunhui
• 0
4
votes
5
replies
317
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
12 days ago • updated 3 days ago
Chris
▴ 10
1,000 results • Page
1 of 20
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards
• All
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Koen Van den Berge
▴ 180
Popular Question
to
shepherl
3.9k
Popular Question
to
Ken C
• 0
Popular Question
to
Johannes Rainer
★ 2.0k
Locations
• All
Sweden,
3 minutes ago
Ireland,
5 minutes ago
United States,
19 minutes ago
Spain,
26 minutes ago
UPF, Barcelona, Spain,
28 minutes ago
Traffic: 410 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