Showing : DESeq2 • reset
17
votes
11
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40k
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DESeq2 and shrinkage of log2 fold changes
deseq2
updated 10 months ago by 43k • written 9.3 years ago by ▴ 100
3
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6
replies
30k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.6 years ago by • 0
5
votes
3
replies
28k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.3 years ago by ▴ 30
10
votes
20
replies
24k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 6 months ago by 68k • written 5.9 years ago by ▴ 30
38
votes
23
replies
17k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
10.6 years ago • updated 5 weeks ago Michael Love 43k
34
votes
29
replies
16k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 7 months ago by 43k • written 10.1 years ago by ▴ 130
0
votes
9
replies
16k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 6.2 years ago by • 0
8
votes
9
replies
15k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 6 hours ago by • 0 • written 8.7 years ago by ▴ 20
16
votes
12
replies
8.6k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 7 months ago by • 0 • written 9.1 years ago by ▴ 60
8
votes
5
replies
7.8k
views
Understanding interaction term in DESeq2
deseq2 design formula log fold change
updated 8 months ago by 43k • written 4.7 years ago by ▴ 40
17
votes
9
replies
7.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 months ago by 68k • written 8.9 years ago by ▴ 10
6
votes
3
replies
7.0k
views
DESeq2 with proteomics data
deseq2
updated 7 months ago by 43k • written 6.8 years ago by ▴ 10
1
vote
7
replies
6.7k
views
DESeq2 with unbalanced experimental design
deseq2
updated 6 months ago by • 0 • written 10.1 years ago by • 0
5
votes
30
replies
5.9k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2 multiple time points time course casecontrol model design
updated 25 days ago by • 0 • written 7.8 years ago by ▴ 10
1
vote
3
replies
5.7k
views
DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 4 weeks ago by • 0 • written 6.4 years ago by • 0
2
votes
3
replies
5.0k
views
Deseq2 use fpkm
deseq2
updated 10 months ago by 43k • written 8.5 years ago by ▴ 40
1
vote
3
replies
4.9k
views
Log2 fold change value in DESeq2
deseq2 rnaseq
written 7.5 years ago by • 0
6
votes
19
replies
4.8k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 12 months ago by • 0 • written 5.6 years ago by ▴ 10
0
votes
8
replies
4.5k
views
DESeq2: handling NA values in colData
deseq2 coldata NA
updated 8 months ago by 43k • written 6.7 years ago by ▴ 170
1
vote
5
replies
4.1k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2 dataframe ensembl gene id gene symbol entrezid
updated 6 weeks ago by • 0 • written 5.4 years ago by ▴ 10
1
vote
8
replies
3.9k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 7.1 years ago by ▴ 60
3
votes
5
replies
3.4k
views
Plot PC1 and PC4 in plotPCA function
DESeq2 plotPCA
updated 10 months ago by • 0 • written 3.2 years ago by • 0
6
votes
5
replies
3.2k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 3 months ago by ▴ 20 • written 8 months ago by • 0
3
votes
6
replies
3.1k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 10 months ago by ★ 4.8k • written 2.1 years ago by ▴ 20
1
vote
2
replies
2.9k
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
12 months ago Patadù ▴ 20
1
vote
2
replies
2.7k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
10 months ago sropri • 0
1
vote
3
replies
2.7k
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
0
votes
2
replies
2.6k
views
DESeq2 Design controlling for gender
deseq2 multiple factor design
updated 20 hours ago by • 0 • written 7.6 years ago by • 0
0
votes
2
replies
2.6k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 11 months ago by • 0 • written 2.3 years ago by ▴ 10
1
vote
8
replies
2.5k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
21 days ago • updated 18 days ago ktz • 0
1
vote
9
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2.5k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 10 months ago by 68k • written 10 months ago by ▴ 10
1
vote
2
replies
2.5k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 10 months ago by ▴ 40 • written 5.5 years ago by • 0
1
vote
3
replies
2.5k
views
ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
DESeq2
updated 5 months ago by 43k • written 2.8 years ago by • 0
2
votes
3
replies
2.3k
views
Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 9 months ago by • 0
3
votes
4
replies
2.3k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 9 weeks ago by • 0 • written 2.9 years ago by ▴ 20
1
vote
5
replies
2.3k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 8 months ago by ▴ 70 • written 3.8 years ago by ▴ 60
1
vote
8
replies
2.3k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 weeks ago • updated 16 days ago Luca • 0
2
votes
3
replies
2.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 2 days ago by • 0 • written 2.5 years ago by ▴ 50
2
votes
7
replies
2.2k
views
DeSeq2 - Can't fetch any results: Error in .wrap_in_length_one_list_like_object(value, name, x)
deseq2 software error
updated 5 months ago by • 0 • written 5.4 years ago by ▴ 30
5
votes
3
replies
2.2k
views
DeSeq2 Comparing One group vs Two groups
DESeq2
written 3.5 years ago by ▴ 10
3
votes
7
replies
2.1k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 8 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 20
0
votes
6
replies
2.0k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
written 7.2 years ago by • 0
0
votes
5
replies
2.0k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.9 years ago by • 0
4
votes
5
replies
2.0k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 10 months ago by • 0 • written 2.1 years ago by ▴ 10
1
vote
6
replies
1.9k
views
how to analysis htseq-count
deseq2
written 7.3 years ago by ▴ 30
0
votes
11
replies
1.9k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 23 days ago by • 0 • written 5 months ago by • 0
6
votes
15
replies
1.9k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
0
votes
9
replies
1.9k
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 10 months ago by ▴ 70 • written 11 months ago by • 0
0
votes
4
replies
1.8k
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
1
vote
5
replies
1.8k
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 10 weeks ago by • 0 • written 7.0 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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