Showing : DEseq2 • reset
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bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
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998
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DESeq2 interaction design
DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
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4
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.3 years ago Eva ▴ 10
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4
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DESeq2 "Not full rank" and "Less than full rank" Errors with design ~ time + ind.nested + time:ind.nested
DESeq2
2.3 years ago Erika • 0
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803
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Model matrix not full rank
DESeq2
2.3 years ago isabelle.dupanloup • 0
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823
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Differential expression analysis with 7 factors (levels) at once?
DESeq2
2.3 years ago melander • 0
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854
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DESeq2: full model matrix is less than full rank
DESeq2
2.3 years ago melander • 0
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4.1k
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
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1.4k
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.3 years ago anne.hoffrichter • 0
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1.1k
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Multi factor design and removing the effect of sex on main factor
DESeq2
2.3 years ago Mahendra • 0
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2
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3.1k
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DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
2.3 years ago Marina • 0
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3
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1.2k
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DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
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2.0k
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Same few genes repeated in DESeq2 Results
DESeq2
2.3 years ago dsambo ▴ 10
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1.4k
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DESeq2 analysis
DESe DESeq2
2.3 years ago Adèle • 0
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
2.3 years ago Luca • 0
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704
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Using DEseq2 for two conditions with different dispersions
DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
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827
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Can't get working R 3.6.3 and 4.2.3 with DESEq2 if compiled by AMD CLANG at Ubuntu 22.04 x64
CLANG DESeq2
2.3 years ago lokapal • 0
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I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
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1.4k
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Deseq2 Results are different using batch design
DESeq2
2.3 years ago hemantcnaik • 0
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827
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Building Multifactor Model in DESeq2
DESeq2
2.3 years ago Abhishek Singh ▴ 20
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11
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3.1k
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Unable to install DESeq2
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.4 years ago Matteo • 0
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1.8k
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Creating heatmaps with 2 Log Fold Changes in DESEQ2
DESeq2
written 2.4 years ago by • 0
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Tximport - Is transcript level expression sum equal to summarisetogene() results
tximpor DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
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DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
2.4 years ago Bushra • 0
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4
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1.3k
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lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
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1.2k
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Specifying design in DESeqDataSetFromMatrix
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
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1.6k
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DESeq2 LRT Reduced Formula
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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558
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Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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1.5k
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DESeq2 not replicable results
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
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912
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p-value<0.05 for a gene with zero counts?
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
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723
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Running DEseq2 without "factor" gives unexpected results
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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1.3k
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DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 17 months ago by 43k • written 2.4 years ago by • 0
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
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Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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962
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Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
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Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.4 years ago by ▴ 20 • written 3.1 years ago by ▴ 20
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DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 20 months ago by ★ 13k • written 2.4 years ago by ▴ 10
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Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.4 years ago Ndimensional ▴ 20
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Identify highly variable genes after vst
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
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5
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DESeq2 design formula
designformula DESeq2
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
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1.2k
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really low padj value from DESeq2
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
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1.0k
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DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
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plotCounts label each sample
p DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
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Heat Map
ColData pheatmap DESeq2
written 2.4 years ago by • 0
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Choosing between VST and rlog for PCA for outlier identification in DESeq2 when small number of samples
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
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3
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1.1k
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Normalization of different input materials
Normalization DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
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Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 30
4,839 results • Page 11 of 97
Recent ...
Replies
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"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
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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