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GLM
•
reset
2
votes
12
replies
2.4k
views
LAPACK/BLAS error with edgeR GLM
glm
edger
lapack
segfault
ruvseq
8.8 years ago
Mark.Rogers
• 0
11
votes
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
8.5 years ago
dietahanson
▴ 30
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
18
votes
10
replies
7.0k
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
▴ 170
2
votes
8
replies
1.6k
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger
GLM
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
alihakimzadeh73
• 0
6
votes
8
replies
2.8k
views
edgeR vs glm.nb
edgeR
glm
8.8 years ago
dongamit123
▴ 20
9
votes
7
replies
1.7k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
8.0 years ago
gergely.zsuzsa.n
• 0
4
votes
7
replies
1.1k
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR
nested
glm
glmQLFit
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
jcalis
▴ 10
4
votes
7
replies
2.6k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2
GLM
timecourse
updated 6.5 years ago by
Michael Love
41k • written 7.3 years ago by
rahel14350
▴ 10
6
votes
6
replies
8.1k
views
EdgeR design matrix with 3 factors
edger
glm
rnaseq
6.4 years ago
Denniswu
▴ 20
3
votes
6
replies
973
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
874
views
Rescaling predictors in DESeq changes outcomes?
deseq2
glm
rescale
updated 3.9 years ago by
Michael Love
41k • 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
1
vote
6
replies
1.6k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR
R
methylation
GLM
4.7 years ago
sabrina.mcnew
• 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
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
0
votes
4
replies
1.2k
views
edgeR GLM design question: contrasts
edger
GLM
8.2 years ago
jwi
• 0
8
votes
4
replies
5.7k
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
1
vote
3
replies
1.2k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2
negative binomial model
glm
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
jeremy.teitelbaum
• 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
11
votes
3
replies
1.7k
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
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
2
votes
2
replies
2.5k
views
order of covariates for GLM with edgeR
edger
differential expression
covariate
batch effect
glm
updated 8.3 years ago by
Gordon Smyth
50k • written 8.4 years ago by
aec
▴ 90
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
1
vote
2
replies
981
views
Treating 2 coefficients as the same group in Limma
limma
glm
updated 7.5 years ago by
James W. MacDonald
65k • written 7.5 years ago by
Ahdee
▴ 50
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 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
jvera8888
• 0
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
2
votes
2
replies
867
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
2
replies
867
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
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2
glm
zinbwave
ruvseq
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
Jakub
▴ 50
1
vote
1
reply
773
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 22 months ago by
Michael Love
41k • written 22 months ago by
stew
• 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
41k • written 6.3 years ago by
serpalma.v
▴ 60
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
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
41k • written 4.4 years ago by
ananda2
• 0
0
votes
1
reply
883
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
rmash
▴ 20
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
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
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
0
replies
832
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
39 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
• 0
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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