Showing : DeSeq2 • reset
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 3 hours ago by ★ 4.4k • written 4 hours ago by • 0
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2
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200
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 2 days ago by 42k • written 7 days ago by ▴ 10
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2
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470
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 2 days ago by 42k • written 9 days ago by • 0
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2
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248
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 2 days ago by 42k • written 14 days ago by ▴ 10
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2
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168
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 5 days ago by ▴ 210 • written 5 days ago by • 0
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1
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191
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 10 days ago by 42k • written 10 days ago by • 0
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6.7k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 14 days ago by 67k • written 8.3 years ago by ▴ 10
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190
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
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2
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429
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 21 days ago by ★ 1.4k • written 26 days ago by • 0
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5
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1.6k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.4 years ago by • 0
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6
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1.3k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 22 days ago by 42k • written 25 days ago by • 0
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6
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26k
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Deseq: What does "BaseMean" mean?
deseq2
written 6.0 years ago by • 0
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2
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750
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 4 weeks ago by ★ 1.4k • written 4 weeks ago by • 0
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11
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641
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
4 weeks ago boczniak767 ▴ 740
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4
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342
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Gene filtering in DESeq2
DESeq2
updated 4 weeks ago by ★ 4.4k • written 4 weeks ago by • 0
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328
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 4 weeks ago by • 0
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2
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235
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Deseq2 - differenc in results
DESeq2
written 4 weeks ago by • 0
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7
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513
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DESeq design with and without intercept is giving different results
DESeq2
written 5 weeks ago by • 0
1
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5
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665
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 5 weeks ago by 51k • written 5 weeks ago by • 0
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3
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369
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 5 weeks ago by • 0
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3
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427
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 5 weeks ago by 51k • written 5 weeks ago by • 0
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2
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261
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 5 weeks ago by • 0
6
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3
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 5 weeks ago by 67k • written 6 weeks ago by • 0
3
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3
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488
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
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2
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468
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R is Removing the Gene Names in My Count Data
DESeq2
updated 6 weeks ago by ▴ 70 • written 6 weeks ago by • 0
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4
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754
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
7 weeks ago • updated 27 days ago Bob • 0
0
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1
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269
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Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
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3
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371
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 weeks ago by • 0
3
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5
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702
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
2
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1
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299
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DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 7 weeks ago by ★ 4.4k • written 7 weeks ago by • 0
2
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2
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401
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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
7 weeks ago BioinfGuru ▴ 70
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500
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
8 weeks ago • updated 7 weeks ago DL • 0
0
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3
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
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15
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1.2k
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 7 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
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2
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657
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
8 weeks ago grothmn • 0
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492
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
4
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7
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936
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 8 weeks ago by ▴ 10 • written 12 weeks ago by ▴ 70
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472
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 8 weeks ago by 42k • written 10 weeks ago by • 0
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1
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557
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 8 weeks ago by 42k • written 9 weeks ago by • 0
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3
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663
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Comparing one group against multiple groups in DESeq2
DESeq2
written 8 months ago by • 0
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 9 weeks ago by • 0
3
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6
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699
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 weeks ago by • 0
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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 10 weeks ago by ▴ 10
0
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3
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477
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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 9 weeks ago by ★ 4.4k • written 9 weeks ago by • 0
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3
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505
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
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10
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958
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Two treatments, one control
DESeq2 stageR
11 weeks ago • updated 10 weeks ago alephreish • 0
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961
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How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
10 weeks ago Fiona • 0
2
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3
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470
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 10 weeks ago by • 0
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304
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 10 weeks ago by ★ 4.4k • written 10 weeks ago by • 0
4
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12
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860
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DGE with a Continuous Variable
DESeq2 model
updated 9 weeks ago by 42k • written 10 weeks ago by • 0
50 results • Page 1 of 1
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Answer: DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plo by ATpoint ★ 4.4k
There is nothing unusual here. There is simply no evidence for differential expression. Almost all genes are shrunken towards zero, due to …
Comment: EdgeR - Apparent Wrong Direction of logFC with Low Count Data by blmurphy • 0
Hi Gordon. It was collation with my edgeR results, BASTA taxonomy, and function gene annotation tables. Prior to doing this last check for …
Answer: Poor dispersion fit in DESeq2 by Michael Love 42k
The fit (red line) doesn't matter because you have so many samples. Note there is almost no shrinkage. Besides that you may be intereste…
Answer: DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days p by Michael Love 42k
I'd recommend actually meeting with a local statistician to work out the analysis plan, or someone familiar with linear models in R. I h…
Answer: DESeq2 design and contrasts with 2 drug-treated and one control group by Michael Love 42k
> Now I am interested in comparing the DE genes between the resistant and acute groups, but I am unsure how to account for DMSO in that com…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
Comment: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
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