Popular Question
Created A Question With More Than 1,000 Views
Awarded 7444 times (see all awards). Earned by the
following contributors:
2 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Issues with installation status of R package rtracklayer
2 years, 9 months ago
Germany/Heidelberg/German Cancer Resear…
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
2 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
3 years, 4 months ago
Germany/Heidelberg/German Cancer Resear…
Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments
3 years, 4 months ago
Germany/Heidelberg/German Cancer Resear…
Implementation of MultiAssayExperiment and curatedTCGAData R packages for quering and prosessing multi-omics cancer datasets
3 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
4 years ago
Germany/Heidelberg/German Cancer Resear…
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
4 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
4 years, 2 months ago
Germany/Heidelberg/German Cancer Resear…
Weird error in Rstudio trying to retreive and load genomic data from external databases
5 years ago
Germany/Heidelberg/German Cancer Resear…
Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
5 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Taking into account strong batch effect in microarray differential expression analysis with limma
5 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Merge different datasets regarding a common number of DE genes in R
5 years, 3 months ago
Germany/Heidelberg/German Cancer Resear…
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
5 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
5 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Correct implementation of multifactorial paired analysis in limma software package for DE expression
5 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
5 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Background correction in Illumina beadchip microarrays with limma neqc function
5 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Explanation of mroast results for specific biological processes and error with barcodeplot function with a microarray dataset
5 years, 6 months ago
Germany/Heidelberg/German Cancer Resear…
Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
5 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Correct assumptions of using limma moderated t-test
5 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
Error in PCA analysis and with ggbiplot function
5 years, 7 months ago
Germany/Heidelberg/German Cancer Resear…
How to analyze correctly agilent two-colour microarray data from the ArrayExpress repository with the limma R package
5 years, 8 months ago
Germany/Heidelberg/German Cancer Resear…
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
5 years, 8 months ago
Germany/Heidelberg/German Cancer Resear…
Include and implement a new reference genome option in the R package BSgenome for downstream variant calling analysis
5 years, 9 months ago
Germany/Heidelberg/German Cancer Resear…
Problem with the colors in the heatmap.2 function and the color key values range
5 years, 9 months ago
Germany/Heidelberg/German Cancer Resear…
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
5 years, 9 months ago
Germany/Heidelberg/German Cancer Resear…
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
5 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
5 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
5 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Questions in limma about multifactorial design and possible batch effect correction
5 years, 11 months ago
Germany/Heidelberg/German Cancer Resear…
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
6 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
6 years, 5 months ago
Germany/Heidelberg/German Cancer Resear…
Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Error in PCA analysis and with ggbiplot function
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Important r packages not available for R version 3.1.1
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Problems importing Illumina raw data with lumi R package
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Update R in Rstudio to specific version 3.2.1 in windows
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Questions in limma about multifactorial design and possible batch effect correction
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Correct assumptions of using limma moderated t-test
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Correct implementation of multifactorial paired analysis in limma software package for DE expression
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
(Gene-set)Pathway analysis based on network/pathway topology in R
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
6 years, 10 months ago
Germany/Heidelberg/German Cancer Resear…
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
6 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 ago
Germany/Heidelberg/German Cancer Resear…
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
7 years ago
Germany/Heidelberg/German Cancer Resear…
Problem with GEOquery R package in Windows when trying to download specific GEO processed data
7 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
7 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
Merge different datasets and perform differential expression analysis in limma
7 years, 1 month ago
Germany/Heidelberg/German Cancer Resear…
Update R in Rstudio to specific version 3.2.1 in windows
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6