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Created An Answer That Has Been Accepted
Awarded 4952 times (see all awards). Earned by the
following contributors:
1 year ago
WEHI, Melbourne, Australia
Answer: Question about transforming log expression values to antilog values in limma
1 year ago
WEHI, Melbourne, Australia
Answer: RNA-Seq normalization of pre and post treatment groups
1 year, 1 month ago
WEHI, Melbourne, Australia
Answer: Question about filter by expression (filterByExpr) in edgeR
1 year, 1 month ago
WEHI, Melbourne, Australia
Answer: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
1 year, 1 month ago
WEHI, Melbourne, Australia
Answer: Repeated Measures-Cross Over Study for RNAseq data using variancePartition::drea
1 year, 1 month ago
WEHI, Melbourne, Australia
Answer: Question about avereps function of limma
1 year, 2 months ago
WEHI, Melbourne, Australia
Answer: do I have to do this step in creating DGEList ?
1 year, 2 months ago
WEHI, Melbourne, Australia
Answer: Reproducibility using limma for DE Analysis
1 year, 3 months ago
WEHI, Melbourne, Australia
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
1 year, 3 months ago
WEHI, Melbourne, Australia
Answer: Processing data with voom "expression values" and "weights"
1 year, 3 months ago
WEHI, Melbourne, Australia
Answer: Estimating Fold-Changes of Lowly Expressed Genes
1 year, 3 months ago
WEHI, Melbourne, Australia
Answer: Limma repeated-measures model: Partial NA coefficients
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: limma: R-squared for time-series data
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: limma plotMDS - logFC inverted?
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Limma, Log2FC and pvalue changing depending on the order of the samples.
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: How to interpret Histogram of average log2 CPM filtering in EdgeR?
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Does negative corfit$consensus cause issues while fitting a model in limma
1 year, 5 months ago
WEHI, Melbourne, Australia
Answer: Too many differentially expressed miRNA with limma
1 year, 5 months ago
WEHI, Melbourne, Australia
Answer: One-tailed test edgeR possible?
1 year, 5 months ago
WEHI, Melbourne, Australia
Answer: Rsubread featureCounts outputs dozens of temp files, no counts
1 year, 6 months ago
WEHI, Melbourne, Australia
Answer: How to visaulize RNAseq data with edgeR, limma, ...?
1 year, 7 months ago
WEHI, Melbourne, Australia
Answer: Question on performing filtering by gene expression on a normalized matrix in li
1 year, 7 months ago
WEHI, Melbourne, Australia
Answer: limma::goana - "Invalid value for odds"
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: Selecting individual samples from tximport and DGE matrix design with missing bi
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: paired samples, comparing expression given a continuous variable
1 year, 9 months ago
WEHI, Melbourne, Australia
Answer: GSVA perfomed on RSEM Expected Count data
1 year, 9 months ago
WEHI, Melbourne, Australia
Answer: How to judge DEG analysis of these samples could be done by using limma::voom
1 year, 9 months ago
WEHI, Melbourne, Australia
Answer: Removing the duplicated genes before limma::voom by using limma::avereps
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: How many features an ExpressionSet can contain ?
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: Stuck on how to voom-limma on RSEM data from TCGA
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: Error in RNAseq123 analysis, unexpected symbol.
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: removeBatchEffect: Coefficients not estimable when using "batch matrix" for `cov
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: Help with constructing design matrix for edgeR/limma
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: LogFC values in edgeR - w/wo intercept
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: Question on RNA-Seq single sample data analysis in EdgeR
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: how to make a group to apply the data to CAMERA
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: Handling NA values in limma's voom design matrix
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: Variance explained (coefficient of determination) in edgeR
2 years ago
WEHI, Melbourne, Australia
Answer: Large difference in PCA plot based on LCPM (log counts per million) and VST (va
2 years ago
WEHI, Melbourne, Australia
Answer: How to make design matrices or compare contrast in limma
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: how to change axis labeling in limma density plot
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: Make samples symbols bigger in PCA / MDS analysis with plotMDS function
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: The number of controls versus treatment in differential expression analysis
2 years, 2 months ago
WEHI, Melbourne, Australia
Answer: Unable to install "limma" package on RStudio
2 years, 2 months ago
WEHI, Melbourne, Australia
Answer: What to do if covariates in design matrix of limma are confounded
2 years, 2 months ago
WEHI, Melbourne, Australia
Answer: Where to find old limma packages not part of a Bioc release?
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