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5
votes
4
replies
2.1k
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 5.6 years ago by ★ 1.1k • written 5.6 years ago by ▴ 830
0
votes
0
replies
849
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger rnaseq paired analysis design matrix
5.6 years ago svlachavas ▴ 830
0
votes
1
reply
1.5k
views
Comment: C: Correct annotation R package for human clariom array analysis
5.7 years ago svlachavas ▴ 830
0
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1
reply
1.5k
views
Comment: C: Correct annotation R package for human clariom array analysis
5.7 years ago svlachavas ▴ 830
1
vote
5
replies
1.5k
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 830
0
votes
0
replies
2.2k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
5.8 years ago svlachavas ▴ 830
0
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1
reply
2.2k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
5.8 years ago svlachavas ▴ 830
0
votes
2
replies
2.2k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
5.8 years ago svlachavas ▴ 830
7
votes
13
replies
2.2k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 5.8 years ago by ★ 7.9k • written 5.8 years ago by ▴ 830
0
votes
1
reply
2.2k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
5.8 years ago svlachavas ▴ 830
3
votes
3
replies
1.4k
views
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat
updated 6.1 years ago by 51k • written 6.1 years ago by ▴ 830
0
votes
0
replies
1.5k
views
Comment: C: Explanation of mroast results for specific biological processes and error with b
6.1 years ago svlachavas ▴ 830
1
vote
2
replies
1.5k
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 6.1 years ago by 51k • written 6.1 years ago by ▴ 830
0
votes
0
replies
1.6k
views
Comment: C: Perform limma based gene-set testing for a two-group comparison in a microarray
6.1 years ago svlachavas ▴ 830
0
votes
0
replies
1.6k
views
Comment: C: Perform limma based gene-set testing for a two-group comparison in a microarray
6.1 years ago svlachavas ▴ 830
2
votes
3
replies
1.6k
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 6.1 years ago by 51k • written 6.1 years ago by ▴ 830
0
votes
1
reply
3.6k
views
Comment: C: How to analyze correctly agilent two-colour microarray data from the ArrayExpres
6.2 years ago svlachavas ▴ 830
1
vote
1
reply
3.6k
views
Comment: C: How to analyze correctly agilent two-colour microarray data from the ArrayExpres
6.2 years ago svlachavas ▴ 830
6
votes
5
replies
3.6k
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 6.2 years ago by 51k • written 6.2 years ago by ▴ 830
0
votes
1
reply
2.3k
views
Comment: C: Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
6.2 years ago svlachavas ▴ 830
0
votes
2
replies
2.3k
views
Answer: A: Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
6.2 years ago svlachavas ▴ 830
0
votes
1
reply
2.1k
views
Comment: C: Include and implement a new reference genome option in the R package BSgenome fo
6.3 years ago svlachavas ▴ 830
0
votes
1
reply
2.1k
views
Comment: C: Include and implement a new reference genome option in the R package BSgenome fo
6.3 years ago svlachavas ▴ 830
3
votes
5
replies
2.1k
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 6.3 years ago by 16k • written 6.3 years ago by ▴ 830
0
votes
0
replies
1.6k
views
Comment: C: Implementation of specific cpm filtering in RNA-Seq data described in a previous
6.4 years ago svlachavas ▴ 830
2
votes
4
replies
1.6k
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger cpm non-specific filtering rnaseq
updated 6.4 years ago by 51k • written 6.4 years ago by ▴ 830
0
votes
0
replies
1.6k
views
Comment: C: Implementation of specific cpm filtering in RNA-Seq data described in a previous
6.4 years ago svlachavas ▴ 830
0
votes
0
replies
3.3k
views
Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
6.4 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
views
Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
6.4 years ago svlachavas ▴ 830
0
votes
0
replies
2.8k
views
Comment: C: Error with R package motifbreakR while trying to read a vcf file with snps.from.
6.4 years ago svlachavas ▴ 830
0
votes
1
reply
2.8k
views
Comment: C: Error with R package motifbreakR while trying to read a vcf file with snps.from.
6.4 years ago svlachavas ▴ 830
1
vote
1
reply
2.6k
views
Answer: A: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
6.4 years ago svlachavas ▴ 830
0
votes
1
reply
2.2k
views
Comment: C: Querying specific TCGA datasets through the MultiAssayExperiment R package
6.4 years ago svlachavas ▴ 830
0
votes
1
reply
2.2k
views
Comment: C: Querying specific TCGA datasets through the MultiAssayExperiment R package
6.4 years ago svlachavas ▴ 830
8
votes
5
replies
2.2k
views
Querying specific TCGA datasets through the MultiAssayExperiment R package
MultiAssayExperiment curatedCRCdata multiomics TCGA
updated 6.4 years ago by 700 • written 6.4 years ago by ▴ 830
0
votes
0
replies
2.8k
views
Comment: C: Error with R package motifbreakR while trying to read a vcf file with snps.from.
6.4 years ago svlachavas ▴ 830
2
votes
5
replies
2.8k
views
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR vcf snps motif analysis
updated 6.4 years ago by ★ 6.8k • written 6.4 years ago by ▴ 830
6
votes
14
replies
3.3k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis variancestabilizingtransformation normalization cpm edger
updated 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 830
0
votes
0
replies
3.3k
views
Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
6.5 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
views
Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
6.5 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
views
Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
6.5 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
views
Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
6.5 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
views
Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
6.5 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
views
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
6.6 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
views
Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
6.6 years ago svlachavas ▴ 830
0
votes
2
replies
3.3k
views
Answer: A: Difficulty in finding DEG using TCGA data from FireBrowse
6.6 years ago svlachavas ▴ 830
0
votes
1
reply
1.0k
views
Comment: C: edgeR multifactorial analysis implementation with RNA-Seq data
6.7 years ago svlachavas ▴ 830
3
votes
3
replies
1.0k
views
edgeR multifactorial analysis implementation with RNA-Seq data
edger multifactorial design multiple comparisons differential gene expression
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 830
0
votes
0
replies
4.0k
views
Comment: C: Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dat
7.0 years ago svlachavas ▴ 830
3
votes
3
replies
4.0k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger DGEList org.hs.eg.db gene annotation
updated 3.2 years ago by • 0 • written 7.0 years ago by ▴ 830
532 results • Page 2 of 11
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