Showing : GLM • reset
1
vote
1
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616
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 17 months ago by 41k • written 17 months ago by • 0
3
votes
6
replies
825
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 3.2 years ago by 64k • written 3.2 years ago by • 0
1
vote
6
replies
753
views
Rescaling predictors in DESeq changes outcomes?
deseq2 glm rescale
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 10
6
votes
6
replies
981
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 3.8 years ago by 13k • written 3.8 years ago by • 0
0
votes
1
reply
744
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 20
0
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1
reply
997
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
7
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5
replies
1.4k
views
EdgeR - Complex design - contrasts/coefficients
edger GLM
updated 4.2 years ago by ▴ 820 • written 4.2 years ago by • 0
1
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6
replies
1.4k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.3 years ago sabrina.mcnew • 0
0
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2
replies
731
views
NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 4.3 years ago by 64k • written 4.3 years ago by • 0
0
votes
3
replies
1.0k
views
ROC curves using normalized sequencing data from 2 experiments
deseq2 pROC ROCR glm
4.5 years ago sebastian.lobentanzer ▴ 50
0
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0
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723
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
4.5 years ago garbuzov • 0
2
votes
8
replies
1.4k
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger GLM
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
4
votes
7
replies
929
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR nested glm glmQLFit
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 10
2
votes
2
replies
744
views
edgeR DEG how many treatments should be fitted to GLM
edgeR GLM
updated 4.9 years ago by 48k • written 4.9 years ago by ▴ 10
0
votes
1
reply
954
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 50
2
votes
2
replies
878
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger glm
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
1
vote
3
replies
1.1k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2 negative binomial model glm
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
9
votes
1
reply
3.9k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 60
6
votes
6
replies
7.8k
views
EdgeR design matrix with 3 factors
edger glm rnaseq
6.0 years ago Denniswu ▴ 20
4
votes
7
replies
2.5k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.1 years ago by 41k • written 6.9 years ago by ▴ 10
5
votes
4
replies
1.2k
views
interpretation of edgeR multi factor conditions in GLM
edger multivariate multiple factor design glm
updated 6.6 years ago by 7.8k • written 6.6 years ago by • 0
2
votes
1
reply
1.1k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 20
1
vote
2
replies
1.4k
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 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
1
vote
2
replies
916
views
Treating 2 coefficients as the same group in Limma
limma glm
updated 7.1 years ago by 64k • written 7.1 years ago by ▴ 50
3
votes
2
replies
5.4k
views
QLF or LRT in edgeR for paired sample designs?
edger paired samples glm QL F-test LR-test
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
11
votes
3
replies
1.6k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.4 years ago by ★ 3.0k • written 7.4 years ago by ▴ 110
3
votes
1
reply
4.8k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger rnaseq glm glmfit
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
9
votes
7
replies
1.5k
views
EdgeR returns small logFC values when using GLM approach
edger glm logfc
7.6 years ago gergely.zsuzsa.n • 0
1
vote
1
reply
1.4k
views
edgeR, DE between 4 different samples
edger differential gene expression GLM Tutorial
updated 7.7 years ago by 64k • written 7.7 years ago by • 0
18
votes
10
replies
6.5k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 7.8 years ago by 48k • written 7.8 years ago by ▴ 170
1
vote
1
reply
2.1k
views
edgeR GLM fitted values
edgeR GLM classification rnaseq
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
0
votes
4
replies
1.1k
views
edgeR GLM design question: contrasts
edger GLM
7.8 years ago jwi • 0
2
votes
2
replies
2.3k
views
order of covariates for GLM with edgeR
edger differential expression covariate batch effect glm
updated 7.9 years ago by 48k • written 8.0 years ago by ▴ 90
11
votes
11
replies
3.1k
views
Different results in edgeR using simple vs GLM
edger glm rnaseq
8.1 years ago dietahanson ▴ 30
2
votes
12
replies
2.3k
views
LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
8.4 years ago Mark.Rogers • 0
6
votes
8
replies
2.5k
views
edgeR vs glm.nb
edgeR glm
8.4 years ago dongamit123 ▴ 20
8
votes
4
replies
5.4k
views
Multiple Comparisons EdgeR
edger multiple comparisons anova glm
updated 8.5 years ago by 7.8k • written 8.5 years ago by ▴ 20
10
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10
replies
6.7k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 8.8 years ago by 48k • written 8.8 years ago by • 0
6
votes
2
replies
1.1k
views
help for designing a multifactorial GLM framework edgeR
edgeR GLM
updated 9.0 years ago by ★ 28k • written 9.0 years ago by • 0
39 results • Page 1 of 1
Recent ...
Replies
Comment: GOslim missing GO term by amanda • 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Comment: GOslim missing GO term by James W. MacDonald 64k
Is this a WGCNA analysis (multiple co-expression clusters sounds like WGCNA)? If so, none of that is inferential or easily interpreted. It …
Comment: GOslim missing GO term by amanda • 0
For each group, I generated multiple co-expression clusters, and within each cluster, cluster PC1 was correlated with PC1 of multiple clini…
Comment: GOslim missing GO term by James W. MacDonald 64k
What do you mean by 'enriched with ... GO terms from their correlations with clinical traits'? Are you doing a GO hypergeometric or somethi…
Comment: GOslim missing GO term by amanda • 0
I have multiple groups to compare with, and each enriched with hundreds of GO terms from their correlations with clinical traits (top1 pval…
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
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