Showing : DEseq2 • reset
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DESeq2 with three factor experimental design
DESeq2 RNASeq
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
6
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7
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4.7k
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DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2 comparison batch
updated 5.0 years ago by • 0 • written 6.3 years ago by • 0
3
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2
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2.4k
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DESeq2 variance stabilizing transformation: why is assay() different from getVarianceStabilizedData()?
DESeq2
5.0 years ago a.giachino2 • 0
0
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5
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2.2k
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DESeq2 with many outliers
DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 10
0
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2
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11k
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Add selected row names on pheatmap
R pheatmap
updated 5.0 years ago by ★ 5.0k • written 5.0 years ago by ▴ 30
0
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4
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946
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Clarifying what results are returned by submitting a list of names to results() when using a user-specified matrix
DESeq2
5.0 years ago thadryan • 0
2
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2
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856
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Normalisation in DESeq2
DESeq2 Normalization
5.0 years ago Bine ▴ 50
7
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6
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5.1k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
5.0 years ago ecg1g15 ▴ 30
6
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6
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3.0k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
5.0 years ago svlachavas ▴ 840
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2
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1.4k
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Compining DESeq2 output with biomart query to display DE genes rather than DE ensembl IDs
DESeq2
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
4
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7
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5.3k
views
DESeq2 DFrame error
DESeq2
updated 4.8 years ago by • 0 • written 5.1 years ago by ▴ 20
2
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1
reply
970
views
Possibility of multi-threading in "estimateDispersions" function
DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
9
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5
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5.2k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
5.0 years ago ecg1g15 ▴ 30
3
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6
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1.9k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 50
0
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2
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1.0k
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Extracting DESeq2 results when using a complex, user-specified matrix and post-hoc significance testing
DESeq2
5.0 years ago thadryan • 0
3
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1
reply
2.5k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 10
0
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1
reply
782
views
Different result when I run Deseq2 in terminal compare to Snakemake
DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
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2
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1.4k
views
Effect of within-group variation on gene expression analysis
DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
4
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3
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2.4k
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Understanding DESeq2 contrasts and p-values
DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 30
8
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7
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13k
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[DESeq2] Best way to select the optimal fitType for dispersion estimates?
deseq2
updated 5.0 years ago by 43k • written 9.6 years ago by ▴ 10
0
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1
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2.5k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 30
2
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4
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3.7k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
5.0 years ago ecg1g15 ▴ 30
0
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5
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1.3k
views
DESeq function fast on laptop but very slow on server
DESeq2
5.0 years ago Saroop • 0
1
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2
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1.5k
views
Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
5
votes
2
replies
16k
views
How to remove dendrogram from pheatmaps?
pheatmapr DESeq2 Bioconductor
updated 5.0 years ago by ★ 4.1k • written 5.0 years ago by • 0
2
votes
5
replies
4.0k
views
Error in lfcShrink
lfcShrink DESeq2
updated 5.0 years ago by ▴ 100 • written 5.1 years ago by • 0
2
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3
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3.0k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 100
0
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2
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1.1k
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p adjusted value not available
StatisticalMethod DESeq2
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
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4
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1.2k
views
DESeq2 interaction study
DESeq2
5.0 years ago sokumoto • 0
0
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3
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4.0k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode : logical
R DESeq2
5.0 years ago Ricard Lambea • 0
2
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1
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2.5k
views
Calculate Cook's cutoff per comparison in DESeq2
Cook'scutoff DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
2
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3
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3.0k
views
lfcshrink() with no coef in resultsNames()
lfcshrink coef DESeq2
updated 4.1 years ago by 43k • written 5.0 years ago by ★ 1.5k
12
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18
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7.5k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 4.7 years ago by 53k • written 5.2 years ago by ▴ 10
8
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8
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2.2k
views
How to shortlist the unaffected gene list from DESeq2 results
DESeq2
updated 4.2 years ago by 43k • written 5.1 years ago by ▴ 20
4
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2
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2.5k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst varianceStabilizingTransformation DESeq2
5.0 years ago Mia ▴ 10
0
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3
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9.5k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
15
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3
replies
2.4k
views
lfcShrink function for different comparison
DESeq2 RNASeq
updated 3.8 years ago by ▴ 30 • written 5.0 years ago by ▴ 90
0
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5
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1.6k
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DESeq2 with 2x2 crossover design
DESeq2 crossover
updated 5.0 years ago by 43k • written 5.1 years ago by • 0
1
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1
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14k
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DESeq Warning Message: Characters converting to factors with desgin
DESeq2
5.0 years ago Amy • 0
1
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1
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1.5k
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DESeq2 Error in checkFullRank(modelMatrix)
DESeq2 ErrorincheckFullRank(modelMatrix) model
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
1
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1
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2.0k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 50
1
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6
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1.2k
views
Time Series: Individuals nested within groups and levels without samples
DESeq2
5.1 years ago • updated 5.0 years ago ijvechetti ▴ 10
0
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2
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861
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Imbalanced samples on paired data using DESeq2
pairedsample DESeq2
5.0 years ago jeffsheng • 0
0
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1
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2.1k
views
Rows do not converge in beta, labelled in mcols(object)$betaConv
DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
6
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7
replies
2.3k
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Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 4.9 years ago by 43k • written 5.1 years ago by ▴ 20
6
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8
replies
5.2k
views
Jitter p-values in volcano plot
EnhancedVolcano DESeq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 20
0
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1
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2.1k
views
Adjust color of ellipse in PCA plot from DESeq2 data set
stat_ellipse DESeq2 ggplot2
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
0
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0
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1000
views
Job: Two Fellowship Positions in Bioinformatics and Toxicology are avaiable immediately at US EPA
job
updated 5.0 years ago by 43k • written 5.1 years ago by • 0
1
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2
replies
1.0k
views
DESeq2 with very large feature set
DESeq2 DifferentialExpression
5.1 years ago ramiro.barrantes ▴ 10
1
vote
1
reply
756
views
What defines a batch in DESeq2 analysis
DESeq2
updated 5.1 years ago by ★ 1.4k • written 5.1 years ago by • 0
4,839 results • Page 34 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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