Showing : DESEq2 • reset
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collided row names in heatmap.2
heatmap.2 genefilter deseq2
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
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Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
4.3 years ago peter.zhouyu • 0
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4
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2.2k
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Batch-corrected expression matrix NOT on a log2 scale
DESeq2 limma
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 70
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5
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1.1k
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Incosistency between contrast and coef parameters in lfcShrink function
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
3
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Compare two samples by Deseqs
DESeq2 RNASeq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
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973
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DESEQ2 - compensating quality difference in replicate samples
DESeq2
4.3 years ago Shail • 0
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1
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1.4k
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Subject paired DESeq2 design
DESeq2 paired design
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
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2.1k
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Relative abundance of differentially abundant ASVs after DESeq2
DESeq2
4.3 years ago Marion • 0
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4
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2.7k
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DESeq2::DESeq(..., parallel = TRUE) fails if a partition has only genes with 0 counts across all samples
DESeq2 BiocParallel
4.3 years ago Steffi Grote ▴ 10
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1.6k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
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Paired samples analysis
DESeq2
4.3 years ago Hanan • 0
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6
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4.4k
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DESeq2 - understanding intercept and contrasts
DESeq2 RNASeq
4.3 years ago sarah-spie ▴ 20
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778
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Interaction terms and selection of coef in normal and shrunk results
DESeq2
4.3 years ago Richelle • 0
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745
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DESeq2, what to do when controls are 7 times more abundant than treatments
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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1.6k
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Warning message of NAs introduced by coercion after nbinomWaldTest
DESeq2
4.3 years ago Richelle • 0
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1.4k
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log2 fold change calculation in deseq2.
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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8
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4.3k
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Combat and dds Object
DESeq2 combat
updated 2.8 years ago by ★ 5.0k • written 4.3 years ago by ▴ 50
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1.4k
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What lfcSE is dependent upon?
DESeq2
written 4.3 years ago by ▴ 10
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1.2k
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P value and Adj. P value showing N/A
DESeq2
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
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2
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DESeq2 Shrinkage methods for scRNA-Seq
DESeq2
4.3 years ago Pedro Tan ▴ 10
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1.5k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.4 years ago • updated 4.3 years ago slcno • 0
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1.1k
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 4.3 years ago by 43k • written 4.4 years ago by • 0
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Using DESEQ2 with selective gene vs all genes
DESeq2
4.4 years ago Shail • 0
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1.6k
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batch effect and size factor differences: vst vs. rlog
DESeq2
4.4 years ago Hannah • 0
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605
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DESeq2 - correct for nested batch with NA values?
DESeq2 deseq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
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3
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2.0k
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vst of DESeq2 for bulk UMI counts
DESeq2 normaliz Normalization
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
2
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1
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1.0k
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Why does samples order subtly influence the results of DESeq2?
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 10
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13
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3.6k
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Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
4.4 years ago RDoc ▴ 10
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2.0k
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DESeq2, geometric means using posCounts
DESeq2
4.4 years ago Phil ▴ 10
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1.6k
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DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
DESeq2 Diffbind
updated 4.4 years ago by ★ 5.2k • written 4.4 years ago by ▴ 10
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4
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DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2 DRIMSeq dtu RNASeq
4.4 years ago sbcn ▴ 80
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Differential Expression analysis of specific list of genes
DESeq2
updated 4.4 years ago by ★ 13k • written 4.4 years ago by ▴ 10
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genefilter not available for R v4.1/arm64
DESeq2 genefilter
4.4 years ago jeremymsimon ▴ 20
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11
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1.9k
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Deseq paired samples
DESeq2
updated 4.3 years ago by 43k • written 4.4 years ago by ▴ 10
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5
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4.6k
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Problem with DESeq2 installation using in R 1.4.1717
DESeq2 Problem installation with
updated 4.4 years ago by ▴ 760 • written 4.4 years ago by • 0
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4
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1.3k
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Problems with pulling specific variables
DESeq2
4.4 years ago Bine ▴ 50
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1.9k
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DeSEq2-- error- count matrix
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
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3
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1.4k
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tximport fails when RSEM output options produce files with additional columns?
DESeq2 tximportData tximpor
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
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Idea: Using DESeq2 to test a change in ratio of two genes
DESeq2
updated 4.3 years ago by 43k • written 4.4 years ago by ▴ 20
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9.4k
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error in relevel.default - 'relevel' only for (unordered) factors when setting baseline
DESeq2
4.4 years ago Yihan • 0
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1.2k
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confusion about Deseq2 wording in the vignette ( additive model with main effects only vs interaction )
DESeq2
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 10
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A permanent error in DESeq2
DESeq2
4.4 years ago AZ ▴ 30
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1.9k
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DESeq2 Paired Analysis--Tumor vs Normal
DESeq2
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
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1.6k
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The P-values with lfcShrink and ashr shrinkage estimator
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
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804
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Identifying sample considered in each group
DESeq2
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
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1
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907
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Group-specific condition effect
DESeq2
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
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935
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samples did not decently separate via pcaPlot
pcaplot deseq2
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
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20
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3.7k
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DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
4.4 years ago • updated 4.3 years ago Ming ▴ 380
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deseq2 for TCGA tumor/normal paired sample from multiple patients
deseq2
updated 4.4 years ago by 43k • written 10.1 years ago by • 0
4,840 results • Page 28 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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