Showing : DESEq • reset
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[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 330
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DESeq multifactor design paired analysis
DESeq DESeq
12.6 years ago Natasha ▴ 440
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DESeq Variance Stabilizing Transformation
Clustering DESeq DESeq2 Clustering DESeq DESeq2
updated 12.6 years ago by 43k • written 12.6 years ago by ▴ 50
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DESeq Normalization Question
Normalization DESeq Normalization DESeq
updated 12.6 years ago by ★ 7.9k • written 12.6 years ago by ▴ 290
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heatmap with variance stabilizing transformed expression data in DESeq
DESeq DESeq
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 180
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DEXSeq: subsetting ExonCountSet ?
DESeq DEXSeq DESeq DEXSeq
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 50
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A few questions about DESeq2 (estimation of dispersion and results table)
DESeq DESeq2 DESeq DESeq2
updated 12.6 years ago by 43k • written 12.6 years ago by ▴ 80
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FW: DESeq Design (val1 vs mean (val2, val3, val4))
DESeq DESeq
updated 12.6 years ago by ★ 3.8k • written 12.6 years ago by ▴ 20
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DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood
Normalization DESeq DEXSeq Normalization DESeq DEXSeq
updated 12.6 years ago by ★ 3.8k • written 12.6 years ago by ▴ 40
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RNAseq analyses: to use, or not use, all the samples; that's the question.
PROcess edgeR DESeq PROcess edgeR DESeq
12.6 years ago Aaron Mackey ▴ 200
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3
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DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 330
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EdgeR- how to work PARTIALLY without replicates
edgeR DESeq edgeR DESeq
updated 12.7 years ago by 53k • written 12.7 years ago by ▴ 10
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DESeq: computing 95% CI for negative binomial distribution ?
TimeCourse timecourse DESeq TimeCourse timecourse DESeq
updated 12.7 years ago by 43k • written 12.7 years ago by ▴ 50
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DESeq: computing 95% CI for negative binomial distribution ?
DESeq DESeq
updated 12.7 years ago by 43k • written 12.7 years ago by ▴ 50
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deseq2
DESeq DESeq2 DESeq DESeq2
12.7 years ago Michael Love 43k
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4
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rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 12.7 years ago by ★ 11k • written 12.7 years ago by ★ 13k
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10
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Multifactor analysis with deseq
Normalization DESeq DESeq2 Normalization DESeq DESeq2
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 420
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(no subject)
DESeq DESeq
updated 12.7 years ago by ▴ 20 • written 12.8 years ago by ▴ 30
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5
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DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 12.7 years ago by 43k • written 12.8 years ago by ★ 13k
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7
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Applying DESeq on RSEM output
edgeR DESeq edgeR DESeq
updated 4.7 years ago by • 0 • written 12.7 years ago by ▴ 30
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1.2k
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DESeq pairwise comparisons between conditions within a multi-factor design
DESeq DESeq
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 10
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Difference between EdgeR and DeSeq in library normalization
RNASeq Normalization edgeR DESeq RNASeq Normalization edgeR DESeq
updated 12.7 years ago by ★ 3.8k • written 12.8 years ago by ▴ 330
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3
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DESeq - plotPCA
DESeq DESeq
updated 12.8 years ago by ★ 3.8k • written 12.8 years ago by ★ 13k
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1.6k
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DESeq Design issue
DESeq DESeq
updated 12.9 years ago by ★ 3.8k • written 12.9 years ago by ★ 13k
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2.5k
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Log transformation and left censoring
limma edgeR DESeq limma edgeR DESeq
updated 12.9 years ago by 53k • written 12.9 years ago by ★ 13k
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3
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Getting DESEq results on just one gene
DESeq DESeq
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ▴ 320
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3
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DEXSeq: building exon count set
DESeq DEXSeq DESeq DEXSeq
updated 12.9 years ago by ★ 1.9k • written 12.9 years ago by ▴ 140
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DESeq - working with more than 2 conditions
DESeq DESeq
updated 12.9 years ago by ★ 3.8k • written 12.9 years ago by ▴ 20
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4
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1.2k
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DESeq package error
DESeq DESeq
updated 12.9 years ago by ★ 8.2k • written 12.9 years ago by ▴ 30
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2.1k
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GLM in DEseq
DESeq DESeq
updated 12.9 years ago by ★ 3.8k • written 12.9 years ago by ★ 13k
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5
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filtering before using DESeq
DESeq DESeq
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 190
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2
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2.7k
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DESeq and EdgeR log fold differences
Normalization edgeR DESeq Normalization edgeR DESeq
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 40
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DESeq: GLM for multi-factor and mulit-level designs
DESeq DESeq
updated 13.0 years ago by ★ 7.9k • written 13.0 years ago by ▴ 60
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1.5k
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Experimental design with edgeR and DESeq packages (RNA-seq)
edgeR DESeq edgeR DESeq
updated 13.1 years ago by 53k • written 13.1 years ago by ▴ 50
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1.0k
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DESeq not available
DESeq DESeq
updated 13.1 years ago by ★ 8.2k • written 13.1 years ago by ★ 13k
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edgeR/DESeq for ChIP-seq analysis
edgeR DESeq edgeR DESeq
updated 13.1 years ago by 53k • written 13.1 years ago by ▴ 240
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Is there any prejudice whether to use edgeR or DESeq for differential expression analysis for RNA Seq data
edgeR DESeq edgeR DESeq
updated 13.1 years ago by ▴ 880 • written 13.1 years ago by ▴ 40
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Removing overlapping genes from annotation for RNAseq read count
RNASeq Annotation PROcess DESeq RNASeq Annotation PROcess DESeq
13.1 years ago Guest User ★ 13k
2
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1
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2.3k
views
DESeq package
Proteomics DESeq Proteomics DESeq
updated 13.2 years ago by ▴ 550 • written 13.2 years ago by ▴ 20
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656
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Multi-factor designs with specific comparisons
DESeq DESeq
13.2 years ago Guest User ★ 13k
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3.8k
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mixed-effects analysis within DEseq
RNASeq DESeq RNASeq DESeq
updated 13.2 years ago by ▴ 150 • written 13.2 years ago by ▴ 10
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4
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1.8k
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DESeq diagnostics
RNASeq Normalization DESeq RNASeq Normalization DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 100
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1
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2.9k
views
plotPCA error
RNASeq DESeq RNASeq DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ★ 13k
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4
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1.5k
views
(no subject)
RNASeq Normalization GO DESeq RNASeq Normalization GO DESeq
updated 13.2 years ago by ★ 2.0k • written 13.2 years ago by ▴ 100
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1.2k
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DESeq - skewed MAplots and other problems
RNASeq Normalization GO DESeq RNASeq Normalization GO DESeq
13.2 years ago Michal Lulu ▴ 100
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12
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4.0k
views
DEseq version and R version compatibility
DESeq DESeq
updated 13.2 years ago by ★ 1.7k • written 13.2 years ago by ▴ 280
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0
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957
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ANOVA in edgeR?
edgeR DESeq edgeR DESeq
13.2 years ago Gordon Smyth 53k
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5
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1.1k
views
shan
DESeq DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ★ 2.0k
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0
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963
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DESeq plotting graphs.
DESeq DESeq
13.2 years ago PRAVIN ▴ 10
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2
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1.8k
views
DESeq - working with more than 2 conditions
edgeR DESeq edgeR DESeq
updated 13.2 years ago by ▴ 180 • written 13.2 years ago by ▴ 440
512 results • Page 7 of 11
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Replies
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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