Showing : GLM • reset
1
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1
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780
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 22 months ago by 41k • written 23 months ago by • 0
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
884
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
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
0
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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
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
1
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6
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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
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2
replies
875
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
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0
replies
841
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
0
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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
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
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 ★ 28k • written 5.1 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
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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
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
1
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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
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
6
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6
replies
8.1k
views
EdgeR design matrix with 3 factors
edger glm rnaseq
6.4 years ago Denniswu ▴ 20
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
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
1
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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
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
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
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
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
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
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
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1
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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
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
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
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 50k • written 8.4 years ago by ▴ 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 ★ 7.9k • written 8.9 years ago by ▴ 20
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
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
39 results • Page 1 of 1
Recent ...
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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