Showing : GLM • reset
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
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
10
votes
10
replies
7.0k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 9.2 years ago by 50k • written 9.2 years ago by • 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 50k • written 8.2 years ago by ▴ 180
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 ★ 28k • written 5.0 years ago by • 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
8.1 years ago gergely.zsuzsa.n • 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 5.0 years ago by ★ 28k • written 5.1 years ago by ▴ 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 41k • written 7.3 years ago by ▴ 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
984
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
1
vote
6
replies
883
views
Rescaling predictors in DESeq changes outcomes?
deseq2 glm rescale
updated 3.9 years ago by 41k • written 3.9 years ago by ▴ 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 ★ 13k • written 4.2 years ago by • 0
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
7
votes
5
replies
1.7k
views
EdgeR - Complex design - contrasts/coefficients
edger GLM
updated 4.6 years ago by ▴ 840 • written 4.6 years ago by ▴ 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 ★ 7.9k • written 7.0 years ago by • 0
0
votes
4
replies
1.2k
views
edgeR GLM design question: contrasts
edger GLM
8.3 years ago jwi • 0
8
votes
4
replies
5.8k
views
Multiple Comparisons EdgeR
edger multiple comparisons anova glm
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 20
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 41k • written 5.8 years ago by • 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
1.8k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.8 years ago by ★ 3.3k • written 7.8 years ago by ▴ 110
6
votes
2
replies
1.3k
views
help for designing a multifactorial GLM framework edgeR
edgeR GLM
updated 9.4 years ago by ★ 28k • written 9.4 years ago by • 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 50k • written 8.4 years ago by ▴ 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 ★ 28k • written 7.7 years ago by • 0
1
vote
2
replies
991
views
Treating 2 coefficients as the same group in Limma
limma glm
updated 7.6 years ago by 65k • written 7.6 years ago by ▴ 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 ★ 28k • written 7.1 years ago by • 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 ★ 28k • written 5.4 years ago by ▴ 10
2
votes
2
replies
874
views
edgeR DEG how many treatments should be fitted to GLM
edgeR GLM
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 10
0
votes
2
replies
873
views
NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 4.7 years ago by 65k • written 4.7 years ago by • 0
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 50
1
vote
1
reply
780
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 22 months ago by 41k • written 22 months ago by • 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 41k • written 6.3 years ago by ▴ 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 ★ 28k • written 7.1 years ago by ▴ 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 41k • written 4.4 years ago by • 0
0
votes
1
reply
893
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 20
3
votes
1
reply
5.3k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger rnaseq glm glmfit
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 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 65k • written 8.1 years ago by • 0
1
vote
1
reply
2.2k
views
edgeR GLM fitted values
edgeR GLM classification rnaseq
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
0
votes
0
replies
840
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
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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