Showing : DeSeq2 • reset
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Discrepancies in normalised count data vs unnormalised
DESeq2
9 months ago • updated 8 months ago AMgroup • 0
0
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2
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779
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Design formula for circadian time-course data for vst() function
DESeq2
9 months ago Vishnu • 0
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2
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938
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Analyzing TnSeq data with DESeq2
DESeq2
written 9 months ago by • 0
0
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1
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1.3k
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How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 9 months ago by 43k • written 10 months ago by • 0
0
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2
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775
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Differing results with DESeq2
DESeq2
updated 9 months ago by • 0 • written 9 months ago by • 0
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2
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636
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RNA Seq using Lrt
DESeq2
9 months ago Rob • 0
0
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3
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1.1k
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Log2foldchange strange behavior
DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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1
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1.0k
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WGCNA
WGCNA DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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1
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1.1k
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Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 20
1
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1
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1.4k
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PhD scholar
RNASeqAnalysis DESeq2
updated 9 months ago by 4.3k • written 9 months ago by • 0
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1
reply
522
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 9 months ago by 68k • written 9 months ago by ▴ 30
1
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3
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1.1k
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DESeq - help with pair wise comparisons
DESeq2
9 months ago bd2000 ▴ 30
1
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8
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3.1k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
9 months ago ktz • 0
0
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1
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817
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
4
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6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
1
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4
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835
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
10 months ago Lennie • 0
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4
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1.5k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 10 months ago by • 0
1
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2
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1.3k
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
10 months ago • updated 8 months ago Erika • 0
1
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8
replies
2.9k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
10 months ago • updated 9 months ago Luca • 0
0
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2
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832
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 10 months ago by ▴ 20
0
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1
reply
498
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 10 months ago by 43k • written 10 months ago by • 0
0
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3
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1.0k
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how many significant figures are there in DESeq2 output
DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by ▴ 180
2
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5
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1.5k
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
11 months ago picasa1983 • 0
3
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7
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2.5k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 11 months ago by ▴ 10 • written 6.9 years ago by ▴ 20
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1
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1.3k
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 11 months ago by 68k • written 11 months ago by • 0
1
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1
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733
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
1
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1
reply
473
views
DEseq2 design for additive treatment
DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
2
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2
replies
919
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Plot title for PCA in DESeq2
DESeq2
11 months ago AL • 0
0
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3
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1.1k
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
1
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2
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1.4k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
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1
reply
481
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
0
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3
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909
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 months ago by • 0 • written 11 months ago by • 0
0
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2
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965
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 11 months ago by • 0 • written 11 months ago by • 0
0
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3
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652
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 11 months ago by • 0 • written 11 months ago by • 0
0
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3
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1.1k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 months ago by • 0 • written 12 months ago by ▴ 10
0
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1
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742
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
2
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2
replies
761
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
0
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4
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1.5k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
12 months ago Quang NN ▴ 10
0
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2
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1.6k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
12 months ago Blandine • 0
0
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5
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806
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
0
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4
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1.2k
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
12 months ago Quang NN ▴ 10
2
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5
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970
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Differential variability modelling with vst() expression
limma DESeq2
written 12 months ago by • 0
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3
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1.0k
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 months ago by • 0
2
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9
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1.9k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 months ago Quang NN ▴ 10
1
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1
reply
1.3k
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 12 months ago by 43k • written 12 months ago by • 0
0
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1
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375
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
0
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1
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666
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 12 months ago by 43k • written 13 months ago by • 0
2
votes
1
reply
783
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 12 months ago by 43k • written 13 months ago by • 0
0
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2
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799
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
13 months ago Kucsera • 0
1
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1
reply
594
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
4,846 results • Page 2 of 97
Recent ...
Replies
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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