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glm
•
reset
1
vote
1
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786
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 23 months ago by
Michael Love
42k • written 23 months ago by
stew
• 0
3
votes
6
replies
990
views
EdgeR design matrix with 3 factors
edgeR
glm
RNAseq
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
jackiesalzbank
• 0
1
vote
6
replies
885
views
Rescaling predictors in DESeq changes outcomes?
deseq2
glm
rescale
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
jc.szamosi
▴ 10
6
votes
6
replies
1.2k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq
design
linear model
glm
updated 4.2 years ago by
Steve Lianoglou
★ 13k • written 4.2 years ago by
tmms
• 0
0
votes
1
reply
896
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
rmash
▴ 20
0
votes
1
reply
1.1k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
ananda2
• 0
7
votes
5
replies
1.7k
views
EdgeR - Complex design - contrasts/coefficients
edger
GLM
updated 4.6 years ago by
Yunshun Chen
▴ 840 • written 4.6 years ago by
D
▴ 10
1
vote
6
replies
1.7k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
4.7 years ago
sabrina.mcnew
• 0
0
votes
2
replies
878
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 4.7 years ago by
James W. MacDonald
65k • written 4.7 years ago by
Guillaume Robert
• 0
0
votes
3
replies
1.2k
views
ROC curves using normalized sequencing data from 2 experiments
deseq2
pROC
ROCR
glm
4.9 years ago
sebastian.lobentanzer
▴ 50
0
votes
0
replies
846
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger
RUVseq
RUVr
GLM
RNAseq
4.9 years ago
garbuzov
• 0
2
votes
8
replies
1.6k
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger
GLM
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
alihakimzadeh73
• 0
4
votes
7
replies
1.2k
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR
nested
glm
glmQLFit
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
jcalis
▴ 10
2
votes
2
replies
878
views
edgeR DEG how many treatments should be fitted to GLM
edgeR
GLM
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
zhang.jianhai
▴ 10
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2
glm
zinbwave
ruvseq
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
Jakub
▴ 50
2
votes
2
replies
1.0k
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger
glm
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
jspmccain
▴ 10
1
vote
3
replies
1.3k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2
negative binomial model
glm
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
jeremy.teitelbaum
• 0
9
votes
1
reply
4.4k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2
model.matrix
GLM
contrast
updated 6.3 years ago by
Michael Love
42k • written 6.3 years ago by
serpalma.v
▴ 60
6
votes
6
replies
8.1k
views
EdgeR design matrix with 3 factors
edger
glm
rnaseq
6.4 years ago
Denniswu
▴ 20
4
votes
7
replies
2.7k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2
GLM
timecourse
updated 6.5 years ago by
Michael Love
42k • written 7.3 years ago by
rahel14350
▴ 10
5
votes
4
replies
1.4k
views
interpretation of edgeR multi factor conditions in GLM
edger
multivariate
multiple factor design
glm
updated 7.0 years ago by
Ryan C. Thompson
★ 7.9k • written 7.0 years ago by
gamaliel.lysander.cabria
• 0
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic
estimate dispersion value
glm
no replicates
deseq
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
hwick1
▴ 20
1
vote
2
replies
1.5k
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 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
jvera8888
• 0
1
vote
2
replies
997
views
Treating 2 coefficients as the same group in Limma
limma
glm
updated 7.6 years ago by
James W. MacDonald
65k • written 7.6 years ago by
Ahdee
▴ 50
3
votes
2
replies
5.8k
views
QLF or LRT in edgeR for paired sample designs?
edger
paired samples
glm
QL F-test
LR-test
updated 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
Akira Imamoto
• 0
11
votes
3
replies
1.8k
views
Fit a multinomial to RNA-seq count data
voom
limma
glm
multinomial
regression
updated 7.8 years ago by
Robert Castelo
★ 3.3k • written 7.8 years ago by
rubi
▴ 110
3
votes
1
reply
5.3k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger
rnaseq
glm
glmfit
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
alessia.donato
• 0
9
votes
7
replies
1.7k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
8.1 years ago
gergely.zsuzsa.n
• 0
1
vote
1
reply
1.5k
views
edgeR, DE between 4 different samples
edger
differential gene expression
GLM
Tutorial
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
wendy_11
• 0
18
votes
10
replies
7.1k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger
estimatedispersions
glm
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
maltethodberg
▴ 180
1
vote
1
reply
2.2k
views
edgeR GLM fitted values
edgeR
GLM
classification
rnaseq
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Mattia
▴ 10
0
votes
4
replies
1.2k
views
edgeR GLM design question: contrasts
edger
GLM
8.3 years ago
jwi
• 0
2
votes
2
replies
2.5k
views
order of covariates for GLM with edgeR
edger
differential expression
covariate
batch effect
glm
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
aec
▴ 90
11
votes
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
8.6 years ago • updated 8.5 years ago
dietahanson
▴ 30
2
votes
12
replies
2.5k
views
LAPACK/BLAS error with edgeR GLM
glm
edger
lapack
segfault
ruvseq
8.8 years ago
Mark.Rogers
• 0
6
votes
8
replies
2.8k
views
edgeR vs glm.nb
edgeR
glm
8.8 years ago
dongamit123
▴ 20
8
votes
4
replies
5.8k
views
Multiple Comparisons EdgeR
edger
multiple comparisons
anova
glm
updated 8.9 years ago by
Ryan C. Thompson
★ 7.9k • written 8.9 years ago by
chickenchamp4
▴ 20
10
votes
10
replies
7.0k
views
GLM Likelihood ratio test
rnaseq
edgeR
GLM
updated 9.2 years ago by
Gordon Smyth
50k • written 9.2 years ago by
ygowtha
• 0
6
votes
2
replies
1.3k
views
help for designing a multifactorial GLM framework edgeR
edgeR
GLM
updated 9.4 years ago by
Aaron Lun
★ 28k • written 9.4 years ago by
damiano.porcelli
• 0
39 results • Page
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Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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