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1
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0
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450
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
8 months ago svlachavas ▴ 830
0
votes
0
replies
680
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.2 years ago svlachavas ▴ 830
0
votes
0
replies
671
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
2.5 years ago svlachavas ▴ 830
5
votes
9
replies
1.6k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.8 years ago by 65k • written 2.8 years ago by ▴ 830
6
votes
6
replies
2.2k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
2.9 years ago svlachavas ▴ 830
5
votes
5
replies
3.2k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.2 years ago by 3.8k • written 3.3 years ago by ▴ 830
3
votes
4
replies
1.8k
views
Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments
MultiAssayExperiment curatedTCGAData TCGAutils
3.4 years ago svlachavas ▴ 830
3
votes
3
replies
1.2k
views
Error in MAE experiment regarding the replacement of internal assays with different number of features
MultiAssayExperiment curatedTCGAData TCGAutils
updated 3.4 years ago by 690 • written 3.4 years ago by ▴ 830
6
votes
6
replies
2.3k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
3.4 years ago svlachavas ▴ 830
3
votes
3
replies
1.3k
views
Implementation of MultiAssayExperiment and curatedTCGAData R packages for quering and prosessing multi-omics cancer datasets
MultiAssayExperiment curatedTCGAData TCGAutils
updated 3.4 years ago by 690 • written 3.5 years ago by ▴ 830
0
votes
0
replies
621
views
Interpretation of mroast p-value results for gene set testing of specific molecular signatures using microarray data
mroast camera gene set testing
3.6 years ago svlachavas ▴ 830
2
votes
5
replies
3.2k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect limma rna seq DE
updated 4.0 years ago by ★ 13k • written 4.0 years ago by ▴ 830
3
votes
5
replies
2.1k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 830
5
votes
5
replies
1.2k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 830
2
votes
4
replies
1.3k
views
Weird error in Rstudio trying to retreive and load genomic data from external databases
R software error Bioconductor
4.2 years ago svlachavas ▴ 830
4
votes
5
replies
1.1k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
4.2 years ago svlachavas ▴ 830
5
votes
4
replies
1.8k
views
Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
curatedTCGAData MultiAssayExperiment multiomics TCGA
updated 5.1 years ago by ★ 1.1k • written 5.1 years ago by ▴ 830
0
votes
0
replies
711
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger rnaseq paired analysis design matrix
5.1 years ago svlachavas ▴ 830
1
vote
5
replies
1.2k
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 830
7
votes
13
replies
1.9k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 5.3 years ago by ★ 7.9k • written 5.3 years ago by ▴ 830
3
votes
3
replies
1.2k
views
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 830
1
vote
2
replies
1.3k
views
Explanation of mroast results for specific biological processes and error with barcodeplot function with a microarray dataset
limma mroast agilent microarrays GO.BP barcodeplot
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 830
2
votes
3
replies
1.4k
views
Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
limma agilent microarrays mroast fry gene tests gene set testing
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 830
6
votes
5
replies
3.2k
views
How to analyze correctly agilent two-colour microarray data from the ArrayExpress repository with the limma R package
agilent microarrays limma arrayexpress NChannelSet
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 830
3
votes
5
replies
1.8k
views
Include and implement a new reference genome option in the R package BSgenome for downstream variant calling analysis
bsgenome variant calling whole exome sequence gencode reference genome
updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 830
2
votes
4
replies
1.3k
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger cpm non-specific filtering rnaseq
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 830
8
votes
5
replies
1.9k
views
Querying specific TCGA datasets through the MultiAssayExperiment R package
MultiAssayExperiment curatedCRCdata multiomics TCGA
updated 5.8 years ago by 690 • written 5.8 years ago by ▴ 830
2
votes
5
replies
2.5k
views
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR vcf snps motif analysis
updated 5.9 years ago by ★ 6.8k • written 5.9 years ago by ▴ 830
6
votes
14
replies
2.9k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis variancestabilizingtransformation normalization cpm edger
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 830
3
votes
3
replies
866
views
edgeR multifactorial analysis implementation with RNA-Seq data
edger multifactorial design multiple comparisons differential gene expression
updated 6.1 years ago by ★ 28k • written 6.2 years ago by ▴ 830
3
votes
3
replies
3.6k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger DGEList org.hs.eg.db gene annotation
updated 2.6 years ago by • 0 • written 6.4 years ago by ▴ 830
6
votes
11
replies
3.0k
views
Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
tcgabiolinks rnaseq normalization EDASeq
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 830
0
votes
0
replies
1.4k
views
Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
edgeR rnaseq DEanalysis TCGA independent filtering
6.4 years ago svlachavas ▴ 830
0
votes
0
replies
1.1k
views
Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarr…
limma batch effect design matrix microarray confounding
7.0 years ago svlachavas ▴ 830
0
votes
0
replies
1.3k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
7.0 years ago svlachavas ▴ 830
2
votes
2
replies
1.6k
views
Problem with GEOquery R package in Windows when trying to download specific GEO processed data
geoquery affymetrix microarrays windows8 getGEO
updated 7.1 years ago by 21k • written 7.1 years ago by ▴ 830
2
votes
3
replies
1.6k
views
Problem with memory limit in Rstudio/Windows when importing Affymetrix HTA 2.0 CEL files with oligo R package
oligo hta2.0 affymetrix microarrays memory problem
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 830
6
votes
7
replies
3.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 23 months ago by ▴ 10 • written 7.1 years ago by ▴ 830
3
votes
1
reply
9.7k
views
Error using function NbClust regarding multiple values in the argument "index" of package NbClust for getting the optimal number of clusters of a dat…
NbClust clustering looping list object function creation
updated 7.1 years ago by ▴ 20 • written 8.6 years ago by ▴ 830
3
votes
4
replies
1.5k
views
Appropriate design matrix set up in limma for 2-factor approches with NA values for specific levels
limma multiple factor design NA values design and contrast matrix
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 830
6
votes
4
replies
1.7k
views
Weird error with raw data using function boxplot after importing Affymetrix Human ST 2.0 CEL files with oligo
microarray affymetrix Human ST arrays oligo hugene20sttranscriptcluster.db
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 830
3
votes
6
replies
1.3k
views
Possible approach of compare/interpret RNA-Seq results with microarray gene expression describing the same phenotype
microarray rnaseq DEgenes meta-analysis limma
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 830
9
votes
6
replies
3.9k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray oligo affycoretools pd.hugene.2.0.st hugene20sttranscriptcluster.db
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 830
25
votes
37
replies
11k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 7.3 years ago by 50k • written 7.3 years ago by ▴ 830
1
vote
4
replies
2.5k
views
Possible transcription factor binding site enrichment analysis in R/Bioconductor and alternative suggestions
transcription factor binding site enrichment analysis bioconductor promoter analysis microarray
updated 7.4 years ago by ★ 13k • written 9.0 years ago by ▴ 830
1
vote
1
reply
1.6k
views
Inspection of batch effect correction success with ComBat in R, regarding a merged dataset comprised of 4 different batches
affymetrix microarrays sva combat sva batch effect plotMDS
updated 7.7 years ago by ▴ 650 • written 7.7 years ago by ▴ 830
0
votes
1
reply
1.3k
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 7.8 years ago by ▴ 420 • written 7.8 years ago by ▴ 830
0
votes
0
replies
979
views
Help in interpreting the plot of the function plotRLDF in limma package for microarray dataset concerning two categorical classes
limma plotRLDF microarray classification linear discriminant function
7.9 years ago svlachavas ▴ 830
0
votes
1
reply
1.0k
views
Questions about the correct implementation of the function plotRLDF from R package limma regarding classification of a microarray dataset
limma microarray plotRLDF classification
7.9 years ago svlachavas ▴ 830
5
votes
10
replies
4.3k
views
Interpretation of results for treat & topTreat functions from limma regarding microarray abalysis
limma treat topTreat microarray
updated 8.0 years ago by 50k • written 8.0 years ago by ▴ 830
121 results • Page 1 of 3
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