Showing : DeSeq2 • reset
0
votes
1
reply
577
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
2
replies
776
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
0
votes
5
replies
2.2k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.4 years ago by • 0
3
votes
6
replies
1.9k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
3
votes
6
replies
31k
views
Deseq: What does "BaseMean" mean?
deseq2
written 7.0 years ago by • 0
0
votes
2
replies
1.5k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
4
votes
11
replies
1.5k
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
13 months ago boczniak767 ▴ 740
3
votes
4
replies
762
views
Gene filtering in DESeq2
DESeq2
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
0
votes
2
replies
702
views
Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 13 months ago by • 0
1
vote
2
replies
466
views
Deseq2 - differenc in results
DESeq2
written 13 months ago by • 0
0
votes
7
replies
1.0k
views
DESeq design with and without intercept is giving different results
DESeq2
written 13 months ago by • 0
1
vote
5
replies
1.4k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 13 months ago by 53k • written 13 months ago by • 0
0
votes
3
replies
1.0k
views
More significant genes after lfcShrink in DEseq2?
DESeq2
written 13 months ago by • 0
0
votes
3
replies
872
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 13 months ago by 53k • written 13 months ago by • 0
0
votes
2
replies
630
views
Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 13 months ago by • 0
6
votes
5
replies
4.0k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 9 months ago by ▴ 20 • written 13 months ago by • 0
3
votes
3
replies
1.5k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
2
replies
1.1k
views
R is Removing the Gene Names in My Count Data
DESeq2
updated 13 months ago by ▴ 70 • written 13 months ago by • 0
1
vote
4
replies
1.4k
views
Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
14 months ago • updated 13 months ago Bob ▴ 30
0
votes
1
reply
551
views
Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
3
replies
966
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 13 months ago by • 0
3
votes
5
replies
2.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 13 months ago by ★ 1.4k • written 14 months ago by • 0
2
votes
1
reply
1.5k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
2
votes
2
replies
808
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
13 months ago BioinfGuru ▴ 70
1
vote
2
replies
767
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
14 months ago • updated 13 months ago DL • 0
0
votes
3
replies
825
views
RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 14 months ago by 68k • written 14 months ago by • 0
6
votes
15
replies
2.3k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 13 months ago by ★ 1.4k • written 14 months ago by • 0
1
vote
2
replies
1.2k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
14 months ago grothmn • 0
0
votes
1
reply
1.2k
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 14 months ago by 68k • written 14 months ago by • 0
4
votes
7
replies
2.1k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 14 months ago by ▴ 10 • written 15 months ago by ▴ 70
0
votes
1
reply
781
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
1
reply
943
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 14 months ago by 43k • written 14 months ago by • 0
2
votes
3
replies
949
views
Comparing one group against multiple groups in DESeq2
DESeq2
written 20 months ago by • 0
2
votes
3
replies
2.9k
views
Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 14 months ago by • 0
3
votes
6
replies
1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 14 months ago by • 0
4
votes
3
replies
1.5k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 14 months ago by ▴ 10
0
votes
3
replies
930
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 14 months ago by ★ 4.9k • written 14 months ago by • 0
1
vote
3
replies
883
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
10
replies
2.0k
views
Two treatments, one control
DESeq2 stageR
15 months ago • updated 14 months ago alephreish • 0
0
votes
2
replies
1.9k
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
14 months ago Fiona • 0
2
votes
3
replies
881
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 14 months ago by • 0
0
votes
1
reply
1.1k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 14 months ago by ★ 4.9k • written 14 months ago by • 0
4
votes
12
replies
1.7k
views
DGE with a Continuous Variable
DESeq2 model
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
2
replies
722
views
DESeq2: two conditions two genotypes
DESeq2
15 months ago • updated 14 months ago Rocio • 0
2
votes
4
replies
1.2k
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 14 months ago by • 0
0
votes
1
reply
905
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
1
reply
466
views
unreal negative log2fc values
DESeq2 des
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
1
reply
512
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
1
vote
8
replies
1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 15 months ago by 53k • written 15 months ago by • 0
1
vote
2
replies
3.1k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
15 months ago sropri • 0
4,835 results • Page 4 of 97
Recent ...
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
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to Joseph • 0
Popular Question to zhe ▴ 20
Popular Question to Natalia • 0
Locations • All
WEHI, Melbourne, Australia, 7 minutes ago
Germany, 57 minutes ago
Spain, 1 hour ago
Barcelona, Spain, 4 hours ago
Mexico, 4 hours ago
Traffic: 824 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