Showing : glm • reset
3
votes
6
replies
192
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 9 months ago by 57k • written 9 months ago by • 0
1
vote
6
replies
148
views
Rescaling predictors in DESeq changes outcomes?
deseq2 glm rescale
updated 12 months ago by 33k • written 12 months ago by ▴ 10
6
votes
6
replies
236
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 16 months ago by 13k • written 16 months ago by • 0
0
votes
1
reply
136
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 18 months ago by 33k • written 18 months ago by • 0
0
votes
1
reply
251
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 18 months ago by 33k • written 18 months ago by • 0
7
votes
5
replies
376
views
EdgeR - Complex design - contrasts/coefficients
edger GLM
updated 21 months ago by ▴ 750 • written 21 months ago by • 0
1
vote
6
replies
281
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
22 months ago • updated 21 months ago sabrina.mcnew • 0
0
votes
2
replies
190
views
NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 22 months ago by 57k • written 22 months ago by • 0
0
votes
3
replies
226
views
ROC curves using normalized sequencing data from 2 experiments
deseq2 pROC ROCR glm
2.0 years ago sebastian.lobentanzer ▴ 50
0
votes
0
replies
261
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
2.0 years ago garbuzov • 0
2
votes
8
replies
501
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger GLM
updated 2.1 years ago by ★ 26k • written 2.1 years ago by • 0
4
votes
7
replies
303
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR nested glm glmQLFit
updated 2.2 years ago by ★ 26k • written 2.2 years ago by ▴ 10
2
votes
2
replies
257
views
edgeR DEG how many treatments should be fitted to GLM
edgeR GLM
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
votes
1
reply
364
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 2.5 years ago by 33k • written 2.5 years ago by ▴ 30
2
votes
2
replies
327
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger glm
updated 2.5 years ago by ★ 26k • written 2.5 years ago by ▴ 10
1
vote
3
replies
483
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2 negative binomial model glm
updated 2.9 years ago by 33k • written 2.9 years ago by • 0
7
votes
1
reply
1.2k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 3.4 years ago by 33k • written 3.4 years ago by ▴ 60
6
votes
6
replies
6.4k
views
EdgeR design matrix with 3 factors
edger glm rnaseq
3.5 years ago Denniswu ▴ 20
4
votes
7
replies
1.4k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 3.6 years ago by 33k • written 4.5 years ago by ▴ 10
5
votes
4
replies
654
views
interpretation of edgeR multi factor conditions in GLM
edger multivariate multiple factor design glm
updated 4.1 years ago by 7.6k • written 4.1 years ago by • 0
2
votes
1
reply
711
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 4.2 years ago by ★ 26k • written 4.2 years ago by ▴ 20
1
vote
2
replies
950
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 4.3 years ago by ★ 26k • written 4.3 years ago by • 0
1
vote
2
replies
551
views
Treating 2 coefficients as the same group in Limma
limma glm
updated 4.7 years ago by 57k • written 4.7 years ago by ▴ 50
3
votes
2
replies
2.8k
views
QLF or LRT in edgeR for paired sample designs?
edger paired samples glm QL F-test LR-test
updated 4.8 years ago by ★ 26k • written 4.8 years ago by • 0
11
votes
3
replies
966
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 4.9 years ago by ★ 2.7k • written 4.9 years ago by ▴ 90
2
votes
1
reply
2.8k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger rnaseq glm glmfit
updated 4.9 years ago by ★ 26k • written 4.9 years ago by • 0
9
votes
7
replies
959
views
EdgeR returns small logFC values when using GLM approach
edger glm logfc
5.2 years ago gergely.zsuzsa.n • 0
1
vote
1
reply
1.0k
views
edgeR, DE between 4 different samples
edger differential gene expression GLM Tutorial
updated 5.2 years ago by 57k • written 5.2 years ago by • 0
19
votes
10
replies
4.3k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 140
1
vote
1
reply
1.4k
views
edgeR GLM fitted values
edgeR GLM classification rnaseq
updated 5.3 years ago by ★ 26k • written 5.3 years ago by ▴ 10
0
votes
4
replies
731
views
edgeR GLM design question: contrasts
edger GLM
5.4 years ago jwi • 0
2
votes
2
replies
1.6k
views
order of covariates for GLM with edgeR
edger differential expression covariate batch effect glm
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 70
11
votes
11
replies
2.2k
views
Different results in edgeR using simple vs GLM
edger glm rnaseq
5.7 years ago • updated 5.6 years ago dietahanson ▴ 30
2
votes
12
replies
1.4k
views
LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
5.9 years ago Mark.Rogers • 0
6
votes
8
replies
1.7k
views
edgeR vs glm.nb
edgeR glm
5.9 years ago dongamit123 ▴ 20
7
votes
4
replies
3.6k
views
Multiple Comparisons EdgeR
edger multiple comparisons anova glm
updated 6.0 years ago by 7.6k • written 6.0 years ago by ▴ 10
10
votes
10
replies
4.3k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
6
votes
2
replies
777
views
help for designing a multifactorial GLM framework edgeR
edgeR GLM
updated 6.5 years ago by ★ 26k • written 6.5 years ago by • 0
38 results • Page 1 of 1
Recent ...
Replies
Answer: How to convert .CEL file to .VCF file? by James W. MacDonald 57k
I don't know of anything within Bioconductor, but after a Google search for affy2vcf (hint), I came upon [this github repo][1]. [1]:…
Answer: DESeq2: One or more designs for contrasts of interest by Michael Love 33k
Sorry, I can only provide software support at this time. I don’t have time to provide statistical consultation on the support site. I’d rec…
Answer: DESeq2 - one groups with no replicates by Michael Love 33k
You can perform this analysis, it should run in DESeq2, but I believe there are also some specialized methods to give a single sample somet…
Answer: failing to install the package org.Hs.eg.db in R (version 4.0.5 ) by James W. MacDonald 57k
You need to supply more than just the error. But anyway, upgrade to R-4.1.0 and Bioconductor 3.13 and see if that fixes the problem.
Answer: Unable to install bioconductor packages by Mike Smith ★ 5.0k
There looks like maybe two different problems here. Let's try fixing the installation of **BiocManager** first, and then maybe everything …
Votes
Answer: DESeq2 - one groups with no replicates
Answer: DESeq2 - one groups with no replicates
pairwise combining factors or multifactor analysis ? (DESeq2)
Comment: Confusion using edgeR and spline-fitted data
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
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