Showing : glm • reset
1
vote
1
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528
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 15 months ago by 40k • written 15 months ago by • 0
3
votes
6
replies
755
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 3.0 years ago by 63k • written 3.0 years ago by • 0
1
vote
6
replies
685
views
Rescaling predictors in DESeq changes outcomes?
deseq2 glm rescale
updated 3.3 years ago by 40k • written 3.3 years ago by ▴ 10
6
votes
6
replies
882
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 3.6 years ago by 13k • written 3.6 years ago by • 0
0
votes
1
reply
695
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 3.8 years ago by 40k • written 3.8 years ago by ▴ 20
0
votes
1
reply
941
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 3.8 years ago by 40k • written 3.8 years ago by • 0
7
votes
5
replies
1.3k
views
EdgeR - Complex design - contrasts/coefficients
edger GLM
updated 4.0 years ago by ▴ 810 • written 4.0 years ago by • 0
1
vote
6
replies
1.2k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.1 years ago sabrina.mcnew • 0
0
votes
2
replies
681
views
NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 4.1 years ago by 63k • written 4.1 years ago by • 0
0
votes
3
replies
959
views
ROC curves using normalized sequencing data from 2 experiments
deseq2 pROC ROCR glm
4.3 years ago sebastian.lobentanzer ▴ 50
0
votes
0
replies
657
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
4.3 years ago garbuzov • 0
2
votes
8
replies
1.3k
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger GLM
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
4
votes
7
replies
833
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR nested glm glmQLFit
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 10
2
votes
2
replies
682
views
edgeR DEG how many treatments should be fitted to GLM
edgeR GLM
updated 4.7 years ago by 48k • written 4.7 years ago by ▴ 10
0
votes
1
reply
886
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 4.8 years ago by 40k • written 4.8 years ago by ▴ 50
2
votes
2
replies
805
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger glm
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 10
1
vote
3
replies
1.0k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2 negative binomial model glm
updated 5.2 years ago by 40k • written 5.2 years ago by • 0
9
votes
1
reply
3.6k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 5.7 years ago by 40k • written 5.7 years ago by ▴ 60
6
votes
6
replies
7.6k
views
EdgeR design matrix with 3 factors
edger glm rnaseq
5.8 years ago Denniswu ▴ 20
4
votes
7
replies
2.4k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 5.9 years ago by 40k • written 6.7 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 6.4 years ago by 7.8k • written 6.4 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 6.5 years ago by ★ 28k • written 6.5 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 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
1
vote
2
replies
885
views
Treating 2 coefficients as the same group in Limma
limma glm
updated 7.0 years ago by 63k • written 7.0 years ago by ▴ 50
3
votes
2
replies
5.2k
views
QLF or LRT in edgeR for paired sample designs?
edger paired samples glm QL F-test LR-test
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
11
votes
3
replies
1.5k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by ▴ 110
3
votes
1
reply
4.7k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger rnaseq glm glmfit
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
9
votes
7
replies
1.5k
views
EdgeR returns small logFC values when using GLM approach
edger glm logfc
7.5 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 7.5 years ago by 63k • written 7.5 years ago by • 0
18
votes
10
replies
6.4k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 7.6 years ago by 48k • written 7.6 years ago by ▴ 170
1
vote
1
reply
2.0k
views
edgeR GLM fitted values
edgeR GLM classification rnaseq
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 10
0
votes
4
replies
1.1k
views
edgeR GLM design question: contrasts
edger GLM
7.7 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 7.8 years ago by 48k • written 7.8 years ago by ▴ 90
11
votes
11
replies
3.0k
views
Different results in edgeR using simple vs GLM
edger glm rnaseq
8.0 years ago • updated 7.9 years ago dietahanson ▴ 30
2
votes
12
replies
2.2k
views
LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
8.2 years ago Mark.Rogers • 0
6
votes
8
replies
2.4k
views
edgeR vs glm.nb
edgeR glm
8.2 years ago dongamit123 ▴ 20
8
votes
4
replies
5.3k
views
Multiple Comparisons EdgeR
edger multiple comparisons anova glm
updated 8.3 years ago by 7.8k • written 8.3 years ago by ▴ 20
10
votes
10
replies
6.5k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 8.6 years ago by 48k • written 8.6 years ago by • 0
6
votes
2
replies
1.1k
views
help for designing a multifactorial GLM framework edgeR
edgeR GLM
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
39 results • Page 1 of 1
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Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles) by Dorien ▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by andrew.b.kleist • 0
This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…
Votes
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
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