Showing : GLM • reset
1
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784
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 23 months ago by 42k • written 23 months ago by • 0
3
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6
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988
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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 42k • written 3.9 years ago by ▴ 10
6
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6
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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
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1
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895
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Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 4.4 years ago by 42k • written 4.4 years ago by ▴ 20
0
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1
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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 42k • written 4.4 years ago by • 0
7
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5
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1.7k
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EdgeR - Complex design - contrasts/coefficients
edger GLM
updated 4.6 years ago by ▴ 840 • written 4.6 years ago by ▴ 10
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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
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876
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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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3
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1.2k
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ROC curves using normalized sequencing data from 2 experiments
deseq2 pROC ROCR glm
4.9 years ago sebastian.lobentanzer ▴ 50
0
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0
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844
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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
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8
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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
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7
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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
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2
replies
878
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 42k • written 5.4 years ago by ▴ 50
2
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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
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1.3k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2 negative binomial model glm
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
9
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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 42k • 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
4
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7
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2.7k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.5 years ago by 42k • written 7.3 years ago by ▴ 10
5
votes
4
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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
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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
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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 ★ 28k • written 7.2 years ago by • 0
1
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2
replies
996
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
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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
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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
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7
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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
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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
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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
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12
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2.5k
views
LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
8.8 years ago Mark.Rogers • 0
6
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8
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2.8k
views
edgeR vs glm.nb
edgeR glm
8.8 years ago dongamit123 ▴ 20
8
votes
4
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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
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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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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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