Showing : DESeq2 • reset
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
3 hours ago • updated 2 hours ago NB • 0
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5
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213
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Identical samples after deseq2 batch effect removal
DESeq2
updated 11 hours ago by 42k • written 1 day ago by • 0
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126
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 1 day ago by 67k • written 1 day ago by • 0
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
2 days ago • updated 1 day ago Denise • 0
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76
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eRNAs count
RNASeq DESeq2
updated 4 days ago by ★ 4.5k • written 4 days ago by • 0
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1
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341
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DESeq2 rerun returns different results
DESeq2
updated 7 days ago by ★ 4.5k • written 7 days ago by • 0
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1
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171
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 8 days ago by 42k • written 9 days ago by • 0
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1
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145
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
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Handling biological replicates in DESeq2
DESeq2
updated 10 days ago by ★ 4.5k • written 11 days ago by • 0
5
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
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6
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 13 days ago by 42k • written 14 days ago by ▴ 10
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324
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 16 days ago by • 0
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
18 days ago • updated 17 days ago LuciaNhu • 0
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1
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358
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Average expression of genes across replicates
DESeq2
updated 19 days ago by ★ 4.5k • written 21 days ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
23 days ago info ▴ 10
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1.2k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
24 days ago • updated 17 days ago Denise • 0
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1
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312
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Deseq to output continous sequencing data
DESeq2
updated 25 days ago by 42k • written 6 weeks ago by • 0
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737
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Adjusted p-values become NA when sub-setting samples
DESeq2
6 weeks ago • updated 16 days ago txema.heredia • 0
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828
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 27 days ago by • 0
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2
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317
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 4 weeks ago by • 0
0
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265
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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987
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Analysis of large RNA-Seq Datasets
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
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720
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DESeq2 - interactions when using factors concatenated into group
DESeq2
5 weeks ago • updated 28 days ago boczniak767 ▴ 740
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181
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
5 weeks ago JY • 0
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260
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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187
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how to extract expression matrix post deseq2
DESeq2
written 5 weeks ago by • 0
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2
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183
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Using Normalized Counts in DESeq2
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
1
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2
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229
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When running contrasts, does it use normalized read counts?
DESeq2
5 weeks ago Katherine • 0
0
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1
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185
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 5 weeks ago by ★ 1.4k • written 6 weeks ago by • 0
3
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4
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454
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
6 weeks ago Eva ▴ 10
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461
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 5 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
0
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1
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166
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
3
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11
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699
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 weeks ago by • 0
2
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4
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387
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 weeks ago jihoon.kim.1495 ▴ 10
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 27 days ago by 42k • written 6 weeks ago by • 0
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4
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425
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
0
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2
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265
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
7 weeks ago • updated 6 weeks ago paul.meraner • 0
0
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0
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177
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
6 weeks ago • updated 23 days ago info ▴ 10
0
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5
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544
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heatmap with batch effect
DESeq2 BatchEffect
7 weeks ago • updated 6 weeks ago tothuhien • 0
0
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2
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343
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
1
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1
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253
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
1
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1
reply
228
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
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1
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318
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 7 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
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2
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434
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 weeks ago by 42k • written 8 weeks ago by ▴ 10
0
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2
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689
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 7 weeks ago by 42k • written 8 weeks ago by • 0
1
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2
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487
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 7 weeks ago by 42k • written 9 weeks ago by ▴ 10
1
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6
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690
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 4 weeks ago by ★ 4.5k • written 8 weeks ago by • 0
0
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1
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289
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 9 weeks ago by 67k • written 8.5 years ago by ▴ 10
0
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1
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279
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Answer: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
Yes. Samples in columns and genes in rows.
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k
It's not informative except for me to say I was right that it's `getSeq` that is providing the error. It appears that `AddMotifs` is passin…
Votes
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
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