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 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
4
votes
7
replies
2.7k
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
987
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
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
993
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 7.2 years ago by ★ 28k • written 7.2 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
877
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
876
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
784
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 23 months ago by 41k • written 23 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
895
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
844
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: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Awards • All
Scholar to Michael Love 41k
Popular Question to Malcolm Cook ★ 1.6k
Teacher to Gordon Smyth 50k
Popular Question to priyanka.m • 0
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
UPF, Barcelona, Spain, 3 minutes ago
Sweden, 6 minutes ago
Finland, 25 minutes ago
France, 27 minutes ago
WEHI, Melbourne, Australia, 29 minutes ago
Traffic: 573 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6