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
Showing :
glm
•
reset
1
vote
1
reply
528
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 15 months ago by
Michael Love
40k • written 15 months ago by
stew
• 0
3
votes
6
replies
755
views
EdgeR design matrix with 3 factors
edgeR
glm
RNAseq
updated 3.0 years ago by
James W. MacDonald
63k • written 3.0 years ago by
jackiesalzbank
• 0
1
vote
6
replies
685
views
Rescaling predictors in DESeq changes outcomes?
deseq2
glm
rescale
updated 3.3 years ago by
Michael Love
40k • written 3.3 years ago by
jc.szamosi
▴ 10
6
votes
6
replies
882
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq
design
linear model
glm
updated 3.6 years ago by
Steve Lianoglou
13k • written 3.6 years ago by
tmms
• 0
0
votes
1
reply
695
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 3.8 years ago by
Michael Love
40k • written 3.8 years ago by
rmash
▴ 20
0
votes
1
reply
941
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 3.8 years ago by
Michael Love
40k • written 3.8 years ago by
ananda2
• 0
7
votes
5
replies
1.3k
views
EdgeR - Complex design - contrasts/coefficients
edger
GLM
updated 4.0 years ago by
Yunshun Chen
▴ 810 • written 4.0 years ago by
D
• 0
1
vote
6
replies
1.2k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
4.1 years ago
sabrina.mcnew
• 0
0
votes
2
replies
681
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 4.1 years ago by
James W. MacDonald
63k • written 4.1 years ago by
Guillaume Robert
• 0
0
votes
3
replies
959
views
ROC curves using normalized sequencing data from 2 experiments
deseq2
pROC
ROCR
glm
4.3 years ago
sebastian.lobentanzer
▴ 50
0
votes
0
replies
657
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger
RUVseq
RUVr
GLM
RNAseq
4.3 years ago
garbuzov
• 0
2
votes
8
replies
1.3k
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger
GLM
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
alihakimzadeh73
• 0
4
votes
7
replies
833
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR
nested
glm
glmQLFit
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
jcalis
▴ 10
2
votes
2
replies
682
views
edgeR DEG how many treatments should be fitted to GLM
edgeR
GLM
updated 4.7 years ago by
Gordon Smyth
48k • written 4.7 years ago by
zhang.jianhai
▴ 10
0
votes
1
reply
886
views
merging RUV-corrected datasets in DESEq
deseq2
glm
zinbwave
ruvseq
updated 4.8 years ago by
Michael Love
40k • written 4.8 years ago by
Jakub
▴ 50
2
votes
2
replies
805
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger
glm
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
jspmccain
▴ 10
1
vote
3
replies
1.0k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2
negative binomial model
glm
updated 5.2 years ago by
Michael Love
40k • written 5.2 years ago by
jeremy.teitelbaum
• 0
9
votes
1
reply
3.6k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2
model.matrix
GLM
contrast
updated 5.7 years ago by
Michael Love
40k • written 5.7 years ago by
serpalma.v
▴ 60
6
votes
6
replies
7.6k
views
EdgeR design matrix with 3 factors
edger
glm
rnaseq
5.8 years ago
Denniswu
▴ 20
4
votes
7
replies
2.4k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2
GLM
timecourse
updated 5.9 years ago by
Michael Love
40k • written 6.7 years ago by
rahel14350
▴ 10
5
votes
4
replies
1.2k
views
interpretation of edgeR multi factor conditions in GLM
edger
multivariate
multiple factor design
glm
updated 6.4 years ago by
Ryan C. Thompson
7.8k • written 6.4 years ago by
gamaliel.lysander.cabria
• 0
2
votes
1
reply
1.1k
views
diffHiC with no biological replicates?
diffhic
estimate dispersion value
glm
no replicates
deseq
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
hwick1
▴ 20
1
vote
2
replies
1.4k
views
Trying to design a model(s) for a two factor RNA-seq experimental analysis in EdgeR with interaction
EdgeR
RNAseq
experimental design
glm
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
jvera8888
• 0
1
vote
2
replies
885
views
Treating 2 coefficients as the same group in Limma
limma
glm
updated 7.0 years ago by
James W. MacDonald
63k • written 7.0 years ago by
Ahdee
▴ 50
3
votes
2
replies
5.2k
views
QLF or LRT in edgeR for paired sample designs?
edger
paired samples
glm
QL F-test
LR-test
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Akira Imamoto
• 0
11
votes
3
replies
1.5k
views
Fit a multinomial to RNA-seq count data
voom
limma
glm
multinomial
regression
updated 7.2 years ago by
Robert Castelo
★ 3.0k • written 7.2 years ago by
rubi
▴ 110
3
votes
1
reply
4.7k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger
rnaseq
glm
glmfit
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
alessia.donato
• 0
9
votes
7
replies
1.5k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
7.5 years ago
gergely.zsuzsa.n
• 0
1
vote
1
reply
1.4k
views
edgeR, DE between 4 different samples
edger
differential gene expression
GLM
Tutorial
updated 7.5 years ago by
James W. MacDonald
63k • written 7.5 years ago by
wendy_11
• 0
18
votes
10
replies
6.4k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger
estimatedispersions
glm
updated 7.6 years ago by
Gordon Smyth
48k • written 7.6 years ago by
maltethodberg
▴ 170
1
vote
1
reply
2.0k
views
edgeR GLM fitted values
edgeR
GLM
classification
rnaseq
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
Mattia
▴ 10
0
votes
4
replies
1.1k
views
edgeR GLM design question: contrasts
edger
GLM
7.7 years ago
jwi
• 0
2
votes
2
replies
2.3k
views
order of covariates for GLM with edgeR
edger
differential expression
covariate
batch effect
glm
updated 7.8 years ago by
Gordon Smyth
48k • written 7.8 years ago by
aec
▴ 90
11
votes
11
replies
3.0k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
8.0 years ago • updated 7.9 years ago
dietahanson
▴ 30
2
votes
12
replies
2.2k
views
LAPACK/BLAS error with edgeR GLM
glm
edger
lapack
segfault
ruvseq
8.2 years ago
Mark.Rogers
• 0
6
votes
8
replies
2.4k
views
edgeR vs glm.nb
edgeR
glm
8.2 years ago
dongamit123
▴ 20
8
votes
4
replies
5.3k
views
Multiple Comparisons EdgeR
edger
multiple comparisons
anova
glm
updated 8.3 years ago by
Ryan C. Thompson
7.8k • written 8.3 years ago by
chickenchamp4
▴ 20
10
votes
10
replies
6.5k
views
GLM Likelihood ratio test
rnaseq
edgeR
GLM
updated 8.6 years ago by
Gordon Smyth
48k • written 8.6 years ago by
ygowtha
• 0
6
votes
2
replies
1.1k
views
help for designing a multifactorial GLM framework edgeR
edgeR
GLM
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
damiano.porcelli
• 0
39 results • Page
1 of 1
Recent ...
Replies
Comment: DiffBind handling of replicates and consensus
by
Rory Stark
★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles)
by
Rory Stark
★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles)
by
Dorien
▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
by
andrew.b.kleist
• 0
This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…
Votes
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Awards
• All
Popular Question
to
Rory Stark
★ 5.0k
Popular Question
to
Stephanie M. Gogarten
▴ 870
Popular Question
to
kicheol.kim
• 0
Teacher
to
ATpoint
★ 3.4k
Popular Question
to
Jitendra
▴ 10
Locations
• All
Netherlands,
2 minutes ago
United States,
8 minutes ago
Russia,
11 minutes ago
United States,
27 minutes ago
Spain,
29 minutes ago
Traffic: 658 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