Showing : DESEq2 • reset
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Best practice for comparing a subset of data /
DESeq2
2.7 years ago TzuChiao ▴ 10
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how can I do gene differential analysis on data after vst
DESeq2
written 2.7 years ago by ▴ 20
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what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 10
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2
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
2.7 years ago Daphnia • 0
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
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832
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.7 years ago garbuzov • 0
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DispEsts plot
DESeq2
2.7 years ago Sep • 0
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Can I run DESeq2 with SMART-Seq data
DESeq2 SMART-seq
2.7 years ago Assa Yeroslaviz ★ 1.5k
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806
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Are polynomial contrasts for a time factor possible in DESeq2?
DESeq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
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796
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deseq2 nested multifactorial analysis
DESeq2 multifactorial nested
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
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Help understanding dispersion values and why so many genes change significance after removing low read samples
DESeq2
2.7 years ago • updated 2.6 years ago Miriam • 0
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DESeqDataSetFromMatrix NA values
DESeq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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How to compute(calculate) rlog and vst provided from DESeq2
DESeq2
2.7 years ago tstpp • 0
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752
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DESeq2 pvalues overly conservative
DESeq2
2.7 years ago gdolsten ▴ 10
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2.0k
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deseq2 RLE normalization
RLE normalization deseq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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Does it make sense to have so many statistically significant gene differentially expressed after DESeq2 paired sample analysis?
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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different number of DEG because of outliers
DESeq2 RNASeq
updated 22 months ago by 53k • written 2.7 years ago by • 0
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colData design issues, need help in R
DESeq2
2.7 years ago R_diot • 0
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755
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DESeq2 paramter inference
DESeq2
2.7 years ago BioEpi • 0
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747
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processing samples with significantly different counts
DESeq2 Normalization
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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5
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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594
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DESeq2 design for time series and control-treated groups
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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2.3k
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DESeq2 Log fold change strange values for certain genes
DESeq2
2.7 years ago Layla • 0
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615
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Time-course for three-factor design
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 740
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901
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DESeq2 with temporal data and different treatments
DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
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929
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DESeq2 won't load
DESeq2 load
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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882
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Accounting for breadth of coverage while using DESeq2
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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816
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DESeq2 for another layer of differential analysis
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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731
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Use of DESeq given unusual experimental data
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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Does the running time of DESeq function is much more longer for design factor containing two variable compare to design factor containing only one v…
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.7 years ago Yang Shi ▴ 10
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5
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1.2k
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Horizontal integration of two RNA-seq datasets derived from two different platforms
DESeq2 dataIntegration
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 20
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5
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.7 years ago by ▴ 760 • written 2.7 years ago by ▴ 10
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1.0k
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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DESeq2 check failure on Linux ARM64
DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
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10
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5.4k
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Is there any chance to solve "the model matrix is not full rank" in DESeq2?
DESeq2
2.7 years ago Sep • 0
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Which samples to remove from analysis based on Cook's distance outliers plot
DESeq2 cooks outliers
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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8
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Understandig listValues argument of DESEQ in multiple group comparisons
DESeq2
updated 2.7 years ago by 43k • written 3.8 years ago by • 0
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958
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Subsetting DESeq when different cell types
DESeq2 RNASeq
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 20
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ColData not reading properly
DESeq2
updated 2.7 years ago by 43k • written 2.8 years ago by • 0
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DESeq2 replicates in time course data
DESeq2 timecoursedata replicates
updated 2.7 years ago by 43k • written 2.8 years ago by • 0
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4
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How do I design my DESEQ experiment?
DESeq2 Metagenomics
2.7 years ago Michael • 0
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DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2 Galaxy pca
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
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7
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Weird dispersion and volcano plots in DEA with paired samples
DESeq2 RNASeq
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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PCA subset of genes vs DE
DESeq2 RNASeq
written 2.8 years ago by ▴ 20
4,839 results • Page 14 of 97
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Replies
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.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
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
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