Showing : DESEq2 • reset
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
20 hours ago • updated 1 minute ago Denise • 0
0
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1
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74
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eRNAs count
RNASeq DESeq2
updated 3 days ago by ★ 4.5k • written 3 days ago by • 0
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1
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335
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DESeq2 rerun returns different results
DESeq2
updated 6 days ago by ★ 4.5k • written 6 days ago by • 0
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1
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166
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 7 days ago by 42k • written 8 days ago by • 0
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1
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135
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 9 days ago by ★ 4.1k • written 9 days ago by • 0
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2
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517
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Handling biological replicates in DESeq2
DESeq2
updated 9 days ago by ★ 4.5k • written 9 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
1
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6
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859
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 12 days ago by 42k • written 12 days ago by ▴ 10
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2
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319
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 15 days ago by • 0
4
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5
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562
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
16 days ago • updated 15 days ago LuciaNhu • 0
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1
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355
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Average expression of genes across replicates
DESeq2
updated 18 days ago by ★ 4.5k • written 19 days ago by • 0
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101
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
21 days ago info ▴ 10
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10
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1.2k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
22 days ago • updated 15 days ago Denise • 0
0
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1
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309
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Deseq to output continous sequencing data
DESeq2
updated 23 days ago by 42k • written 5 weeks ago by • 0
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732
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Adjusted p-values become NA when sub-setting samples
DESeq2
5 weeks ago • updated 14 days ago txema.heredia • 0
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3
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826
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 25 days ago by • 0
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311
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 29 days ago by • 0
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1
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264
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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
2
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3
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983
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Analysis of large RNA-Seq Datasets
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
1
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4
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716
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DESeq2 - interactions when using factors concatenated into group
DESeq2
4 weeks ago • updated 26 days ago boczniak767 ▴ 740
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1
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180
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
5 weeks ago • updated 4 weeks ago JY • 0
0
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1
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259
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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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182
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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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226
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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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183
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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 5 weeks ago by • 0
3
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4
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453
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
5 weeks ago Eva ▴ 10
1
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4
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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 6 weeks ago by • 0
0
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1
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165
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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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695
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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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384
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 weeks ago jihoon.kim.1495 ▴ 10
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6
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783
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 25 days ago by 42k • written 6 weeks ago by • 0
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4
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423
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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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264
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
6 weeks ago paul.meraner • 0
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174
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
6 weeks ago • updated 21 days ago info ▴ 10
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5
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538
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heatmap with batch effect
DESeq2 BatchEffect
6 weeks ago tothuhien • 0
0
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2
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342
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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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250
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
1
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1
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225
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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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316
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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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432
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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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687
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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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486
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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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687
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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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287
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
17
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9
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7.0k
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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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278
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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
0
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2
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496
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 10 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
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5
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1.7k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.5 years ago by • 0
3
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6
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1.4k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 10 weeks ago by 42k • written 11 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differene between the Wald and LRT test for time-series gene expression data by Denise • 0
This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units by elozanoe • 0
Hi! I'm facing the same problem. Is there any easy way to output relative abundances of higher taxonomic units (up to kingdom), similar to…
Answer: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://diendannhansu.com/threads/hayal-sohbet-odalari.667004/ https://forum.realdigital.org/u/serkan https://animefagos.com/miembros/ser…
Comment: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://www.hayalsohbet.net https://www.yerlichat.com https://www.yerlichat.net https://www.mavisim.net https://www.hayalchat.com http…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
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A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
Answer: Differene between the Wald and LRT test for time-series gene expression data
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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