Showing : DESEq2 • reset
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
12 hours ago eric • 0
0
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2
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272
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 5 days ago by ★ 1.4k • written 10 days ago by • 0
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5
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1.5k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.3 years ago by • 0
3
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6
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1.2k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 7 days ago by 42k • written 10 days ago by • 0
3
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6
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25k
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Deseq: What does "BaseMean" mean?
deseq2
written 6.0 years ago by • 0
0
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2
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673
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 15 days ago by ★ 1.4k • written 16 days ago by • 0
4
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11
replies
584
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
18 days ago • updated 16 days ago boczniak767 ▴ 740
3
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4
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314
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Gene filtering in DESeq2
DESeq2
updated 18 days ago by ★ 4.4k • written 18 days ago by • 0
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2
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266
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 19 days ago by • 0
1
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2
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214
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Deseq2 - differenc in results
DESeq2
written 19 days ago by • 0
0
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7
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465
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DESeq design with and without intercept is giving different results
DESeq2
written 21 days ago by • 0
1
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5
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626
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 21 days ago by 51k • written 23 days ago by • 0
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3
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336
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 23 days ago by • 0
0
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3
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401
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 24 days ago by 51k • written 24 days ago by • 0
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2
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246
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 26 days ago by • 0
6
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3
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835
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 25 days ago by 67k • written 27 days ago by • 0
3
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3
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439
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 4 weeks ago by 67k • written 4 weeks ago by • 0
0
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2
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434
views
R is Removing the Gene Names in My Count Data
DESeq2
updated 4 weeks ago by ▴ 70 • written 4 weeks ago by • 0
1
vote
4
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711
views
Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
5 weeks ago • updated 11 days ago Bob • 0
0
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1
reply
254
views
Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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3
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347
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 4 weeks ago by • 0
3
votes
5
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656
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 4 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
2
votes
1
reply
257
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 4 weeks ago by ★ 4.4k • written 4 weeks ago by • 0
2
votes
2
replies
376
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
4 weeks ago BioinfGuru ▴ 70
1
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2
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477
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
5 weeks ago • updated 4 weeks ago DL • 0
0
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3
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347
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
6
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15
replies
1.1k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 5 weeks ago by ★ 1.4k • written 6 weeks ago by • 0
1
vote
2
replies
631
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
6 weeks ago grothmn • 0
0
votes
1
reply
479
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
4
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7
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903
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 5 weeks ago by ▴ 10 • written 10 weeks ago by ▴ 70
0
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1
reply
456
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 6 weeks ago by 42k • written 8 weeks ago by • 0
0
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1
reply
542
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
2
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3
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640
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Comparing one group against multiple groups in DESeq2
DESeq2
written 7 months ago by • 0
2
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3
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694
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 7 weeks ago by • 0
3
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6
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672
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 7 weeks ago by • 0
4
votes
3
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1.1k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 8 weeks ago by ▴ 10
0
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3
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456
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 7 weeks ago by ★ 4.4k • written 7 weeks ago by • 0
1
vote
3
replies
484
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 7 weeks ago by 42k • written 8 weeks ago by • 0
0
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10
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915
views
Two treatments, one control
DESeq2 stageR
9 weeks ago • updated 7 weeks ago alephreish • 0
0
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2
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929
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
8 weeks ago • updated 7 weeks ago Fiona • 0
2
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3
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442
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 8 weeks ago by • 0
0
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1
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263
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 8 weeks ago by ★ 4.4k • written 8 weeks ago by • 0
4
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12
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828
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DGE with a Continuous Variable
DESeq2 model
updated 7 weeks ago by 42k • written 8 weeks ago by • 0
1
vote
2
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408
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DESeq2: two conditions two genotypes
DESeq2
9 weeks ago Rocio • 0
2
votes
4
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566
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DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 9 weeks ago by • 0
0
votes
1
reply
315
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
0
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1
reply
220
views
unreal negative log2fc values
DESeq2 des
updated 10 weeks ago by 67k • written 10 weeks ago by • 0
0
votes
1
reply
310
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
1
vote
8
replies
694
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 9 weeks ago by 51k • written 11 weeks ago by • 0
1
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2
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1.3k
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Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
11 weeks ago sropri • 0
50 results • Page 1 of 1
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Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
The odds ratio, not log FC. My bad.
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
``` testResult$Eff_Condition > 0.1 ```
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Hello, Thank you. I absolutely respect what you mention about p-values and logFC, I was just going to tackle that soon and thank you for po…
Comment: QSEA:Error in h(simpleError(msg, call)) by kf • 0
genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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