Showing : DeSeq2 • reset
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
10 months ago Anna • 0
1
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2
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770
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Deseq2 res Function
DESeq2
updated 10 months ago by 68k • written 10 months ago by ▴ 10
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4
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701
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
10 months ago NB • 0
0
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5
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737
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Identical samples after deseq2 batch effect removal
DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
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1
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550
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 10 months ago by 68k • written 10 months ago by • 0
1
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2
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467
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
10 months ago Denise • 0
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1
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389
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eRNAs count
RNASeq DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
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1
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590
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DESeq2 rerun returns different results
DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
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1
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492
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
reply
496
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
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2
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1.0k
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Handling biological replicates in DESeq2
DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.7 years ago by ▴ 30
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6
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1.5k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 10 months ago by 43k • written 10 months ago by ▴ 10
0
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2
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562
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 11 months ago by • 0
4
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5
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1.3k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
11 months ago LuciaNhu • 0
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1
reply
707
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Average expression of genes across replicates
DESeq2
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
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0
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383
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
11 months ago info ▴ 10
0
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11
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2.3k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 6 months ago by • 0 • written 11 months ago by • 0
0
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1
reply
541
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Deseq to output continous sequencing data
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
1
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4
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1.3k
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Adjusted p-values become NA when sub-setting samples
DESeq2
11 months ago txema.heredia • 0
3
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3
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1.5k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 months ago by • 0
0
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2
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718
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 11 months ago by • 0
0
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1
reply
474
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
2
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3
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1.3k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
1
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4
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1.1k
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DESeq2 - interactions when using factors concatenated into group
DESeq2
11 months ago boczniak767 ▴ 740
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1
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346
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
11 months ago JY • 0
0
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1
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423
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
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2
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461
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how to extract expression matrix post deseq2
DESeq2
written 11 months ago by • 0
0
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2
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492
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Using Normalized Counts in DESeq2
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
3
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2
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556
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When running contrasts, does it use normalized read counts?
DESeq2
11 months ago Katherine ▴ 20
0
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1
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393
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
3
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4
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1.2k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
11 months ago Eva ▴ 10
1
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4
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1.2k
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 11 months ago by ★ 4.9k • written 12 months ago by • 0
0
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1
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485
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
2
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4
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826
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
12 months ago jihoon.kim.1495 ▴ 10
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6
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1.3k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 11 months ago by 43k • written 12 months ago by • 0
5
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4
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939
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 12 months ago by ★ 4.9k • written 12 months ago by • 0
0
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2
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611
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
12 months ago paul.meraner • 0
0
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0
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529
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
12 months ago • updated 11 months ago info ▴ 10
1
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6
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1.3k
views
heatmap with batch effect
DESeq2 BatchEffect
written 12 months ago by • 0
0
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2
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674
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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 12 months ago by 43k • written 12 months ago by • 0
1
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1
reply
937
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
1
reply
533
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 12 months ago by ★ 4.9k • written 12 months ago by • 0
1
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1
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565
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 12 months ago by ★ 4.9k • written 12 months ago by • 0
1
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2
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825
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 12 months ago by 43k • written 12 months ago by ▴ 10
0
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2
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975
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
1
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2
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986
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 12 months ago by 43k • written 12 months ago by ▴ 10
1
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6
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1.7k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 11 months ago by ★ 4.9k • written 12 months ago by • 0
0
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1
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443
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
17
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9
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8.1k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 12 months ago by 68k • written 9.3 years ago by ▴ 10
4,835 results • Page 3 of 97
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Replies
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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