Showing : deseq2 • reset
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
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2
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788
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
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5
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2.2k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.4 years ago by • 0
3
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6
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1.9k
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[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
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6
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32k
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Deseq: What does "BaseMean" mean?
deseq2
written 7.1 years ago by • 0
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2
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1.5k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 13 months ago by ★ 1.4k • written 14 months ago by • 0
4
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11
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1.5k
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
14 months ago • updated 13 months ago boczniak767 ▴ 740
3
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4
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778
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Gene filtering in DESeq2
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
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2
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721
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 14 months ago by • 0
1
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2
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479
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Deseq2 - differenc in results
DESeq2
written 14 months ago by • 0
0
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7
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1.0k
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DESeq design with and without intercept is giving different results
DESeq2
written 14 months ago by • 0
1
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5
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1.4k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 14 months ago by 53k • written 14 months ago by • 0
0
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3
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1.1k
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 14 months ago by • 0
0
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3
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894
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 14 months ago by 53k • written 14 months ago by • 0
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2
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654
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 14 months ago by • 0
6
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5
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4.0k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 9 months ago by ▴ 20 • written 14 months ago by • 0
3
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3
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1.6k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 14 months ago by 68k • written 14 months ago by • 0
0
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2
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1.2k
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R is Removing the Gene Names in My Count Data
DESeq2
updated 14 months ago by ▴ 70 • written 14 months ago by • 0
1
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4
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1.4k
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
14 months ago • updated 13 months ago Bob ▴ 30
0
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1
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575
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Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 14 months ago by 43k • written 14 months ago by • 0
0
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3
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985
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 14 months ago by • 0
3
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5
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2.2k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
2
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1
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1.5k
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DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
2
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2
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836
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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
14 months ago BioinfGuru ▴ 70
1
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2
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775
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
14 months ago DL • 0
0
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3
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846
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 14 months ago by 68k • written 14 months ago by • 0
6
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15
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2.4k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
1
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2
replies
1.2k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
14 months ago grothmn • 0
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1
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1.2k
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 15 months ago by 68k • written 15 months ago by • 0
4
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7
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2.1k
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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
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1
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805
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 15 months ago by 43k • written 15 months ago by • 0
0
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1
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951
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 15 months ago by 43k • written 15 months ago by • 0
2
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3
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967
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Comparing one group against multiple groups in DESeq2
DESeq2
written 21 months ago by • 0
2
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3
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2.9k
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 15 months ago by • 0
3
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6
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1.3k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 15 months ago by • 0
4
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3
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1.6k
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 15 months ago by ▴ 10
0
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3
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955
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
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3
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901
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
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10
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2.0k
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Two treatments, one control
DESeq2 stageR
15 months ago alephreish • 0
0
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2
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1.9k
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How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
15 months ago Fiona • 0
2
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3
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906
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 15 months ago by • 0
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1
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1.1k
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
4
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12
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1.8k
views
DGE with a Continuous Variable
DESeq2 model
updated 15 months ago by 43k • written 15 months ago by • 0
1
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2
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730
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DESeq2: two conditions two genotypes
DESeq2
15 months ago Rocio • 0
2
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4
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1.2k
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DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 15 months ago by • 0
0
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1
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926
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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
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1
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482
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unreal negative log2fc values
DESeq2 des
updated 15 months ago by 68k • written 15 months ago by • 0
0
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1
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529
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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
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8
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1.8k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 15 months ago by 53k • written 16 months ago by • 0
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2
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3.1k
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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
16 months ago sropri • 0
4,835 results • Page 4 of 97
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Answer: Issue with Soft-Thresholding in WGCNA by misty.chickadee.vckc • 0
Hi Maria, your detailed explanation is super helpful! The NA power estimate in WGCNA can be tricky. I've sometimes seen that when the data …
Comment: Interpretation of output of AffyRNAdeg and hist commands by debasainalsa • 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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