Showing : DESEq2 • reset
0
votes
3
replies
742
views
DESeq2 - Comparing Comparisons
DESeq2
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
4
replies
927
views
lfcShrink and alpha value
lfcShrink DESeq2
12 months ago • updated 11 months ago anon • 0
2
votes
1
reply
707
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
2
replies
496
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
2
replies
473
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
12 months ago Anna • 0
1
vote
2
replies
799
views
Deseq2 res Function
DESeq2
updated 12 months ago by 68k • written 12 months ago by ▴ 10
0
votes
4
replies
744
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
12 months ago NB • 0
0
votes
5
replies
762
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
1
reply
573
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
2
replies
491
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
12 months ago Denise • 0
0
votes
1
reply
419
views
eRNAs count
RNASeq DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
votes
1
reply
623
views
DESeq2 rerun returns different results
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
votes
1
reply
525
views
Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
1
reply
591
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
2
votes
2
replies
1.1k
views
Handling biological replicates in DESeq2
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.9 years ago by ▴ 30
1
vote
6
replies
1.6k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 12 months ago by 43k • written 12 months ago by ▴ 10
0
votes
2
replies
577
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 12 months ago by • 0
4
votes
5
replies
1.3k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
12 months ago LuciaNhu • 0
0
votes
1
reply
738
views
Average expression of genes across replicates
DESeq2
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
0
votes
0
replies
412
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
13 months ago info ▴ 10
0
votes
11
replies
2.5k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 7 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
560
views
Deseq to output continous sequencing data
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
vote
4
replies
1.4k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
13 months ago • updated 12 months ago txema.heredia • 0
3
votes
3
replies
1.5k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 13 months ago by • 0
0
votes
2
replies
787
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 13 months ago by • 0
0
votes
1
reply
491
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
2
votes
3
replies
1.3k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
vote
4
replies
1.1k
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
13 months ago boczniak767 ▴ 740
0
votes
1
reply
375
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
13 months ago JY • 0
0
votes
1
reply
469
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
2
replies
491
views
how to extract expression matrix post deseq2
DESeq2
written 13 months ago by • 0
0
votes
2
replies
546
views
Using Normalized Counts in DESeq2
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
3
votes
2
replies
594
views
When running contrasts, does it use normalized read counts?
DESeq2
13 months ago Katherine ▴ 20
0
votes
1
reply
422
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
3
votes
4
replies
1.3k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
13 months ago Eva ▴ 10
1
vote
4
replies
1.3k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 13 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
1
reply
526
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
2
votes
4
replies
898
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
13 months ago jihoon.kim.1495 ▴ 10
0
votes
6
replies
1.4k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 13 months ago by 43k • written 13 months ago by • 0
5
votes
4
replies
1.0k
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 13 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
2
replies
691
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
13 months ago paul.meraner • 0
0
votes
0
replies
597
views
News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
13 months ago info ▴ 10
1
vote
6
replies
1.5k
views
heatmap with batch effect
DESeq2 BatchEffect
written 13 months ago by • 0
0
votes
2
replies
753
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
1
reply
1.0k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
1
reply
692
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
1
reply
596
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
2
replies
884
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 14 months ago by ▴ 10
0
votes
2
replies
1.0k
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
4,839 results • Page 3 of 97
Recent ...
Replies
Comment: Generalized edgeR functions by Omar • 0
[ragdoll hit](https://ragdollhitstickman.io/) That actually sounds like a reasonable approach, especially if the overlapping intervals repr…
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to story.benjamin ▴ 20
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Locations • All
Russia, just now
Vietnam, 47 minutes ago
Vietnam, 1 hour ago
United States, 1 hour ago
The city by the bay, 1 hour ago
Traffic: 1021 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6