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following contributors:
7 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
7 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarray data
7 years, 12 months ago
Germany/Heidelberg/German Cancer Resear…
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
8 years ago
Germany/Heidelberg/German Cancer Resear…
Problem with GEOquery R package in Windows when trying to download specific GEO processed data
8 years ago
Germany/Heidelberg/German Cancer Resear…
Problem with memory limit in Rstudio/Windows when importing Affymetrix HTA 2.0 CEL files with oligo R package
8 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
Update R in Rstudio to specific version 3.2.1 in windows
8 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
Merge different datasets and perform differential expression analysis in limma
8 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
8 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
8 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate design matrix set up in limma for 2-factor approches with NA values for specific levels
8 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Weird error with raw data using function boxplot after importing Affymetrix Human ST 2.0 CEL files with oligo
8 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Possible approach of compare/interpret RNA-Seq results with microarray gene expression describing the same phenotype
8 years, 4 months ago
Germany/Heidelberg/German Cancer Resear…
Possible transcription factor binding site enrichment analysis in R/Bioconductor and alternative suggestions
8 years, 8 months ago
Germany/Heidelberg/German Cancer Resear…
Inspection of batch effect correction success with ComBat in R, regarding a merged dataset comprised of 4 different batches
8 years, 9 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
8 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Help in interpreting the plot of the function plotRLDF in limma package for microarray dataset concerning two categorical classes
8 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Questions about the correct implementation of the function plotRLDF from R package limma regarding classification of a microarray dataset
8 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Interpretation of results for treat & topTreat functions from limma regarding microarray abalysis
9 years ago
Germany/Heidelberg/German Cancer Resear…
Error using function NbClust regarding multiple values in the argument "index" of package NbClust for getting the optimal number of clusters of a dataset
9 years ago
Germany/Heidelberg/German Cancer Resear…
GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
9 years ago
Germany/Heidelberg/German Cancer Resear…
defining a function for multiple paired t.test in many rows of a microarray dataset
9 years ago
Germany/Heidelberg/German Cancer Resear…
Important r packages not available for R version 3.1.1
9 years ago
Germany/Heidelberg/German Cancer Resear…
Appropriate use of the function treat of the limma package
9 years ago
Germany/Heidelberg/German Cancer Resear…
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
9 years ago
Germany/Heidelberg/German Cancer Resear…
Correct assumptions of using limma moderated t-test
9 years ago
Germany/Heidelberg/German Cancer Resear…
Use of various distance measures and clustering methods in heatmap creation
9 years ago
Germany/Heidelberg/German Cancer Resear…
Filtering on present/absent calls methodology and perfect match only arrays
9 years ago
Germany/Heidelberg/German Cancer Resear…
Error in PCA analysis and with ggbiplot function
9 years ago
Germany/Heidelberg/German Cancer Resear…
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
9 years ago
Germany/Heidelberg/German Cancer Resear…
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
9 years ago
Germany/Heidelberg/German Cancer Resear…
Correct creation of design matrix in limma for testing a specific comparison of interest in a microarray dataset
9 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
Error in PCA analysis and with ggbiplot function
9 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Weird error after trying to subset an microarray expression set with gene symbols from topTable function from limma
9 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
9 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Error while calling function topTable() from limma R package in microarray data analysis
9 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
9 years, 4 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate selection of DE list in limma before and after implementation of arrayWeights in conjuction with duplicateCorrelation functions
9 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Background correction arguments in R package GCRMA for microarray pre-processing analysis
9 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
9 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate explanation of the methodology behind arrayWeights function from limma R package
9 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
9 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Possible methodologies of machine learning in R that can assimilate continuous variables along gene expression data for microarray classification
9 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Possible methodologies for missing value imputation of continuous variables in a data frame in R
9 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Possible methodologies for constructing multi-level comparisons in limma
9 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Questions regarding removal and following re-installation of a specific R package using a custom library path
9 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
9 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Problem regarding the explanation of log-fold changes of individual coefficients in limma after eBayes
9 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
9 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Possible(validated) methodology implemented in R for integrating and analyzing clinical data with gene expression data in R
9 years, 8 months ago
Germany/Heidelberg/German Cancer Resear…
Correct creation of design matrix in limma regarding a multi-level experiment
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