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Created An Answer That Has Been Accepted
Awarded 5091 times (see all awards). Earned by the
following contributors:
3 years ago
WEHI, Melbourne, Australia
Answer: Selecting individual samples from tximport and DGE matrix design with missing bi
3 years, 1 month ago
WEHI, Melbourne, Australia
Answer: paired samples, comparing expression given a continuous variable
3 years, 1 month ago
WEHI, Melbourne, Australia
Answer: GSVA perfomed on RSEM Expected Count data
3 years, 2 months ago
WEHI, Melbourne, Australia
Answer: How to judge DEG analysis of these samples could be done by using limma::voom
3 years, 2 months ago
WEHI, Melbourne, Australia
Answer: Removing the duplicated genes before limma::voom by using limma::avereps
3 years, 3 months ago
WEHI, Melbourne, Australia
Answer: How many features an ExpressionSet can contain ?
3 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Stuck on how to voom-limma on RSEM data from TCGA
3 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Error in RNAseq123 analysis, unexpected symbol.
3 years, 3 months ago
WEHI, Melbourne, Australia
Answer: removeBatchEffect: Coefficients not estimable when using "batch matrix" for `cov
3 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Help with constructing design matrix for edgeR/limma
3 years, 4 months ago
WEHI, Melbourne, Australia
Answer: LogFC values in edgeR - w/wo intercept
3 years, 4 months ago
WEHI, Melbourne, Australia
Answer: Question on RNA-Seq single sample data analysis in EdgeR
3 years, 4 months ago
WEHI, Melbourne, Australia
Answer: how to make a group to apply the data to CAMERA
3 years, 4 months ago
WEHI, Melbourne, Australia
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
3 years, 4 months ago
WEHI, Melbourne, Australia
Answer: Handling NA values in limma's voom design matrix
3 years, 4 months ago
WEHI, Melbourne, Australia
Answer: Variance explained (coefficient of determination) in edgeR
3 years, 5 months ago
WEHI, Melbourne, Australia
Answer: Large difference in PCA plot based on LCPM (log counts per million) and VST (va
3 years, 5 months ago
WEHI, Melbourne, Australia
Answer: How to make design matrices or compare contrast in limma
3 years, 5 months ago
WEHI, Melbourne, Australia
Answer: Limma vs. lm for methylation data
3 years, 5 months ago
WEHI, Melbourne, Australia
Answer: how to change axis labeling in limma density plot
3 years, 6 months ago
WEHI, Melbourne, Australia
Answer: Make samples symbols bigger in PCA / MDS analysis with plotMDS function
3 years, 6 months ago
WEHI, Melbourne, Australia
Answer: The number of controls versus treatment in differential expression analysis
3 years, 6 months ago
WEHI, Melbourne, Australia
Answer: Complex contrasts in limma
3 years, 7 months ago
WEHI, Melbourne, Australia
Answer: Unable to install "limma" package on RStudio
3 years, 7 months ago
WEHI, Melbourne, Australia
Answer: What to do if covariates in design matrix of limma are confounded
3 years, 7 months ago
WEHI, Melbourne, Australia
Answer: Where to find old limma packages not part of a Bioc release?
3 years, 7 months ago
WEHI, Melbourne, Australia
Answer: Differential gene expression and (adjusted) p-values
3 years, 8 months ago
WEHI, Melbourne, Australia
Answer: catchKallisto results are not counts
3 years, 9 months ago
WEHI, Melbourne, Australia
Answer: Filtering low coverage RRBS counts results in few reads. Any alternatives?
3 years, 10 months ago
WEHI, Melbourne, Australia
Answer: Multi-level design RRBS analysis with voomLmFit
3 years, 10 months ago
WEHI, Melbourne, Australia
Answer: RMA on different disease labels
3 years, 10 months ago
WEHI, Melbourne, Australia
Answer: Advice to use block factor and duplicatecorrelation in RNA-seq experiment
3 years, 11 months ago
WEHI, Melbourne, Australia
Answer: DESeq2/edgeR/limma help with most appropriate design matrix
3 years, 11 months ago
WEHI, Melbourne, Australia
Answer: edgeR contrasts confusion when multiple groups are involved
4 years ago
WEHI, Melbourne, Australia
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
4 years, 1 month ago
WEHI, Melbourne, Australia
Answer: Query regarding the use of eBayes + topTable and treat + topTreat
4 years, 1 month ago
WEHI, Melbourne, Australia
Answer: Query regarding the use of eBayes + topTable and treat + topTreat
4 years, 1 month ago
WEHI, Melbourne, Australia
Answer: Query regarding the use of eBayes + topTable and treat + topTreat
4 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Complex design with paired and unpaired samples with edgeR RNA-seq DE analysis
4 years, 3 months ago
WEHI, Melbourne, Australia
Answer: lmFit, continuous exposure, adjustment covariates
4 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Use of arrayWeights with two treatment groups
4 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Differential expression error in edgeR - maybe from design matrix?
4 years, 4 months ago
WEHI, Melbourne, Australia
Answer: Optimal edgeR design for a single-factor experiment
4 years, 4 months ago
WEHI, Melbourne, Australia
Answer: The eBayes function gives two p-values for each row
4 years, 4 months ago
WEHI, Melbourne, Australia
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
4 years, 5 months ago
WEHI, Melbourne, Australia
Answer: Pipeline for an Anova-like analysis in edgeR
4 years, 5 months ago
WEHI, Melbourne, Australia
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
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