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Created An Answer That Has Been Accepted
Awarded 4958 times (see all awards). Earned by the
following contributors:
3 weeks ago
WEHI, Melbourne, Australia
Answer: Why p value inconsistent when using different number of pathway score?
3 weeks, 2 days ago
WEHI, Melbourne, Australia
Answer: FilterByExpr low counts with small sample size
1 month ago
WEHI, Melbourne, Australia
Answer: Light difference when using coef vs omit a group when compare 3 groups.
1 month, 1 week ago
WEHI, Melbourne, Australia
Answer: limma models out of memory issue on Slurm HPC
1 month, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Differing results from plotMDS and PCAtools
1 month, 2 weeks ago
WEHI, Melbourne, Australia
Answer: The difference when using Limma compare between 3 conditions vs 2 conditions
1 month, 3 weeks ago
WEHI, Melbourne, Australia
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
1 month, 4 weeks ago
WEHI, Melbourne, Australia
Answer: Question about extracting co-efficients for pairwise comparisons in edgeR
2 months ago
WEHI, Melbourne, Australia
Answer: Constrast for Time Course Experiments using Limma
2 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Confusion about LFC using contrasts weights in EdgeR
2 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Normalization factors when there is a possible unidirectional expression
3 months ago
WEHI, Melbourne, Australia
Answer: How does one test for interactions in EdgeR?
3 months ago
WEHI, Melbourne, Australia
Answer: Design matrix after RUVg correction
3 months ago
WEHI, Melbourne, Australia
Answer: How to get normalized values for methylation counts in edgeR
3 months ago
WEHI, Melbourne, Australia
Answer: Limma design for 3 replicated time courses comparing treatment vs placebo
3 months ago
WEHI, Melbourne, Australia
Answer: voom with quality weights after RUV correction
3 months, 1 week ago
WEHI, Melbourne, Australia
Answer: Using limma for controlling age variable
3 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: [BUG] Rsubread::featureCounts quirk in CORE files: different target list orderin
3 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Monotonic genes in results of differential gene expression analysis
3 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: EdgeR: Should I include all samples/conditions in my dispersion estimation while
3 months, 4 weeks ago
WEHI, Melbourne, Australia
Answer: filtering lowly expressed reads
5 months ago
WEHI, Melbourne, Australia
Answer: removeBatchEffect with non-linear model fit
5 months ago
WEHI, Melbourne, Australia
Answer: Correct the batch effect in methylation analysis in R
5 months, 1 week ago
WEHI, Melbourne, Australia
Answer: Filter genes by expression for voomLmFit
5 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Is it appropriate to apply linear mixed models to Voom transformed data?
5 months, 4 weeks ago
WEHI, Melbourne, Australia
Answer: limma + voom combine voomWithQualityWeights and duplicateCorrelation
6 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: DecideTest vs topTAGs in edgeR
6 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: [Bug] Segfault in edgeR::cpm
7 months ago
WEHI, Melbourne, Australia
Answer: limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsist
7 months ago
WEHI, Melbourne, Australia
Answer: limma: More differentially expressed genes when factor included in model than wh
7 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Batch correction and repeated measures
8 months ago
WEHI, Melbourne, Australia
Answer: EdgeR and DESeq2, variance estimation and parametric test
8 months ago
WEHI, Melbourne, Australia
Answer: Phenotype effect - building a contrast matrix - grouping vs interaction
8 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Import Salmon data with tximport and pool technical replicates
9 months ago
WEHI, Melbourne, Australia
Answer: removing the batch effect for vst counts and defining the batches in removeBatch
9 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Adding a group of samples reduces DEGs in other groups
9 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: loading scores using plotMDS in limma
9 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Grouping DEGs yields varying results
9 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Question about RNAseq analysis in EdgeR to identify common and donor specific di
10 months, 1 week ago
WEHI, Melbourne, Australia
Answer: edgeR, RRBS Library size preparation
10 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Does this RNAseq experiment require a repeated measures approach?
11 months, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Extracting fitted expression matrix from Limma
1 year ago
WEHI, Melbourne, Australia
Answer: edgeR with Successive Differences Contrast Coding?
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