Showing : DEseq2 • reset
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DESeq2 LRT test without a fixed base reference
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
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DESeq2 (version 1.10 vs 1.30)
version1.30 version1.10 deseq2 DESeq2
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by • 0
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Can VST be run without runing DESeq or estimateSizeFactors
DESeq2
4.2 years ago A ▴ 60
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2
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1.4k
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How similar or disimilar are two sets of DEG?
DESeq2 RNASeq
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
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5
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VST transformation and covariates in the TCGA TARGET GTEx dataset
VST TCGATARGETGTEx DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
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8
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deseq2 machine sizing best practices for very large data set
l DESeq2
updated 4.0 years ago by ▴ 20 • written 4.2 years ago by ▴ 20
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2
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"full model matrix is less than full rank"
SQuIRE deseq2 DESeq2
4.2 years ago fernandogs97 ▴ 10
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Understanding output of Negative Binomial in DESeq2
DESeq2
4.2 years ago • updated 4.0 years ago synat.keam • 0
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5
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Combining two groups in contrast deseq2
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 50
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error: cannot execute 'f951': execvp: No such file or directory when downloading DESeq2 package
DESeq2
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by • 0
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1.3k
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Effect size using likelihood ratio test in DESeq2
DESeq2
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by • 0
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2
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2.9k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
4.2 years ago jbnrodriguez ▴ 10
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1.4k
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Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
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2
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3.1k
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Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
4.2 years ago Qin ▴ 10
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2.4k
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Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
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936
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Log fold change interpretation of time series with Wald test
DESeq2
4.2 years ago jd348 • 0
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1
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871
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RNA Seq - Venn Diagramm - display exclusively expressed genes
VennDetail DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
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7
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2.0k
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small dimensions in the matrix of counts from smallRNA using DESEq2
matrix DESeq2 SmallRNA dimensions small
4.2 years ago andreia ▴ 10
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3
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Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 40
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Sequencing depth before and aftr normalisation with DESEQ2 doesn't look as expected: Problem?
normalisation DESEQ2
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by • 0
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Nanostringdiff - defining contrast values for blocking variables in glm
limma edgeR DESeq2 NanoStringDiff
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
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3
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
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1.5k
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What does one-sided p-value in DESeq2 mean in biological terms?
one-sided nbinomWaldTest p-value meta-analysis DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
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6
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1.8k
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DESeq2 design for paired samples
DESeq2 paired
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
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1.7k
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Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 4.2 years ago by ▴ 40 • written 4.2 years ago by • 0
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4
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975
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normalising Biological replicates for differential analysis
DESeq2 Rtudio
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by • 0
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How to calculate dispersion DESeq2 - Step by Step
DGE DESeq2 Differential
4.3 years ago • updated 4.2 years ago Zeke Smith ▴ 10
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952
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pairwise within sample
DESeq2 microbiome
updated 4.2 years ago by 43k • written 4.3 years ago by • 0
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8
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2.9k
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How does the design formula affect dispersion estimate in DESeq2?
deseq2
updated 4.2 years ago by 43k • written 5.2 years ago by ▴ 20
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3
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Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 4.2 years ago by 43k • written 4.3 years ago by • 0
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11
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2.9k
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Recalculated abundance data output table with DEseq2
DESeq2
updated 4.0 years ago by 43k • written 4.3 years ago by • 0
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log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
4.3 years ago Claire • 0
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1.3k
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Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 7.7 years ago by • 0
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3
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1.5k
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Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 4.2 years ago by 43k • written 4.3 years ago by • 0
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4
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1.8k
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
4.3 years ago • updated 4.2 years ago khaveh ▴ 10
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725
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Question about my design
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.6 years ago by • 0 • written 4.3 years ago by ▴ 10
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7
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1.5k
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DESEQ2 log2FC is not following Normalized read count
DESeq2
updated 4.2 years ago by 43k • written 4.3 years ago by • 0
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DESEQ PCA
DESeq2 miRNA
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
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5
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 3.2 years ago by 43k • written 4.3 years ago by • 0
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4
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ylim and xlim in Enhanced Volcano
DESeq2 EnhancedVolcano Bioconductor
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
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DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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755
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How to write design and contrast in DESeq2 to find the up-regulated genes where the design have interactions
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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pairwise comparison + interaction term in DESeq2
DESeq2 interaction pairwise
4.3 years ago Lucas • 0
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4
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3.9k
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weird MAplot or volcano plot of DESeq2 diff result
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 40
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5
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2.2k
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lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 4.2 years ago by 43k • written 4.3 years ago by ▴ 40
4
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9
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DESeq2 paired design
DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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3
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1.5k
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Not full rank DESeq2
DESeq2 DifferentialExpression
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
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1
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979
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Different DESeq2 results
DESeq2 DifferentialExpression
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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1.1k
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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
4,839 results • Page 27 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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