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following contributors:
7 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
7 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
7 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate design matrix set up in limma for 2-factor approches with NA values for specific levels
7 years, 7 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
7 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Possible approach of compare/interpret RNA-Seq results with microarray gene expression describing the same phenotype
7 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Possible transcription factor binding site enrichment analysis in R/Bioconductor and alternative suggestions
8 years 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, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
8 years, 4 months ago
Germany/Heidelberg/German Cancer Resear…
Interpretation of results for treat & topTreat functions from limma regarding microarray abalysis
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Correct assumptions of using limma moderated t-test
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Use of various distance measures and clustering methods in heatmap creation
8 years, 5 months 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
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
defining a function for multiple paired t.test in many rows of a microarray dataset
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate use of the function treat of the limma package
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Important r packages not available for R version 3.1.1
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
8 years, 5 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, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Error in PCA analysis and with ggbiplot function
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Filtering on present/absent calls methodology and perfect match only arrays
8 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Correct creation of design matrix in limma for testing a specific comparison of interest in a microarray dataset
8 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Error in PCA analysis and with ggbiplot function
8 years, 7 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
8 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
8 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Error while calling function topTable() from limma R package in microarray data analysis
8 years, 8 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
8 years, 9 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
8 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
8 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate explanation of the methodology behind arrayWeights function from limma R package
8 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
8 years, 11 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
8 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Possible methodologies for missing value imputation of continuous variables in a data frame in R
8 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Possible methodologies for constructing multi-level comparisons in limma
9 years 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 ago
Germany/Heidelberg/German Cancer Resear…
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
9 years ago
Germany/Heidelberg/German Cancer Resear…
Problem regarding the explanation of log-fold changes of individual coefficients in limma after eBayes
9 years ago
Germany/Heidelberg/German Cancer Resear…
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
9 years 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 ago
Germany/Heidelberg/German Cancer Resear…
Correct creation of design matrix in limma regarding a multi-level experiment
9 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
Annotation Problem regarding double platform merged microarray eset using the inSilicoMerging R package, after differential expression analysis
9 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Possible construction of heatmap for clustering only genes for different treatments and not samples
9 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Possible TF binding site enrichment analysis through mroast and conversion problems
9 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
9 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Annotation problems regarding quality information for Illumina HumanHT-12 v4-illuminaHumanv4.db
9 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Annotation issues with illumina microarray preprocessing with limma
9 years, 4 months ago
Germany/Heidelberg/German Cancer Resear…
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
9 years, 4 months ago
Germany/Heidelberg/German Cancer Resear…
Error while trying to upgrade R to version 3.2
9 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Error in R package "cancerclass" with function nvalidate
9 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Machine learning methods for feature selection and possible correlation with clinical data
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