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Created An Answer That Has Been Accepted
Awarded 5048 times (see all awards). Earned by the
following contributors:
1 year, 2 months ago
WEHI, Melbourne, Australia
Answer: Phenotype effect - building a contrast matrix - grouping vs interaction
1 year, 3 months ago
WEHI, Melbourne, Australia
Answer: Import Salmon data with tximport and pool technical replicates
1 year, 3 months ago
WEHI, Melbourne, Australia
Answer: removing the batch effect for vst counts and defining the batches in removeBatch
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Adding a group of samples reduces DEGs in other groups
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: loading scores using plotMDS in limma
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Grouping DEGs yields varying results
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Question about RNAseq analysis in EdgeR to identify common and donor specific di
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: NA p values in edgeR results
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: edgeR, RRBS Library size preparation
1 year, 5 months ago
WEHI, Melbourne, Australia
Answer: Does this RNAseq experiment require a repeated measures approach?
1 year, 6 months ago
WEHI, Melbourne, Australia
Answer: Extracting fitted expression matrix from Limma
1 year, 6 months ago
WEHI, Melbourne, Australia
Answer: Contrast of Contrasts in Limma
1 year, 7 months ago
WEHI, Melbourne, Australia
Answer: edgeR with Successive Differences Contrast Coding?
1 year, 7 months ago
WEHI, Melbourne, Australia
Answer: Question about transforming log expression values to antilog values in limma
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: RNA-Seq normalization of pre and post treatment groups
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: Question about filter by expression (filterByExpr) in edgeR
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: Repeated Measures-Cross Over Study for RNAseq data using variancePartition::drea
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: Question about avereps function of limma
1 year, 9 months ago
WEHI, Melbourne, Australia
Answer: do I have to do this step in creating DGEList ?
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: Reproducibility using limma for DE Analysis
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: Processing data with voom "expression values" and "weights"
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: Estimating Fold-Changes of Lowly Expressed Genes
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: Limma repeated-measures model: Partial NA coefficients
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: limma: R-squared for time-series data
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: limma plotMDS - logFC inverted?
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: Limma, Log2FC and pvalue changing depending on the order of the samples.
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: How to interpret Histogram of average log2 CPM filtering in EdgeR?
1 year, 12 months ago
WEHI, Melbourne, Australia
Answer: Does negative corfit$consensus cause issues while fitting a model in limma
2 years ago
WEHI, Melbourne, Australia
Answer: Too many differentially expressed miRNA with limma
2 years ago
WEHI, Melbourne, Australia
Answer: Rsubread featureCounts outputs dozens of temp files, no counts
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: How to visaulize RNAseq data with edgeR, limma, ...?
2 years, 2 months ago
WEHI, Melbourne, Australia
Answer: Question on performing filtering by gene expression on a normalized matrix in li
2 years, 2 months ago
WEHI, Melbourne, Australia
Answer: limma::goana - "Invalid value for odds"
2 years, 3 months ago
WEHI, Melbourne, Australia
Answer: Selecting individual samples from tximport and DGE matrix design with missing bi
2 years, 3 months ago
WEHI, Melbourne, Australia
Answer: paired samples, comparing expression given a continuous variable
2 years, 4 months ago
WEHI, Melbourne, Australia
Answer: GSVA perfomed on RSEM Expected Count data
2 years, 4 months ago
WEHI, Melbourne, Australia
Answer: How to judge DEG analysis of these samples could be done by using limma::voom
2 years, 4 months ago
WEHI, Melbourne, Australia
Answer: Removing the duplicated genes before limma::voom by using limma::avereps
2 years, 5 months ago
WEHI, Melbourne, Australia
Answer: How many features an ExpressionSet can contain ?
2 years, 5 months ago
WEHI, Melbourne, Australia
Answer: Stuck on how to voom-limma on RSEM data from TCGA
2 years, 5 months ago
WEHI, Melbourne, Australia
Answer: Error in RNAseq123 analysis, unexpected symbol.
2 years, 6 months ago
WEHI, Melbourne, Australia
Answer: removeBatchEffect: Coefficients not estimable when using "batch matrix" for `cov
2 years, 6 months ago
WEHI, Melbourne, Australia
Answer: Help with constructing design matrix for edgeR/limma
2 years, 6 months ago
WEHI, Melbourne, Australia
Answer: LogFC values in edgeR - w/wo intercept
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