Showing : DEseq2 • reset
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DESeq2 Multiple Comparison Testing with Contrasts
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
3
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12
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2.4k
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
6.8 years ago ariel ▴ 20
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1
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1.0k
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Local versus parametric fitType in DESeq2 in this instance?
deseq2 rna-seq
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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6
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2.6k
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[deseq2] normalization between samples after merging transcripts into genes
deseq2 tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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5
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2.1k
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Hill shape p-value histogram after differential miRNA expression analysis with DESeq2
deseq2 mirna fdrtool
updated 6.8 years ago by ★ 3.4k • written 6.8 years ago by • 0
5
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6
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2.2k
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DESeq2 w. pathway/network info as a prior knowledge
deseq2 pathway ihw
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 20
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1
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1.4k
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Deseq2 padjusted values versus pvalue
deseq2 RNASeq padjusted
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
3
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3
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1.2k
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clarification of time-series analysis
deseq2 baseline LRT
updated 6.8 years ago by 43k • written 6.8 years ago by ★ 1.5k
2
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10
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4.0k
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Time-series analysis with DESeq2
deseq2 time-series design matrix edger
updated 6.8 years ago by 43k • written 6.8 years ago by ★ 1.5k
2
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3
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4.4k
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Differences in contrast results while using DESeq2 for one vs all rest combined conditions
deseq2 rna-seq differential expression analysis
6.8 years ago shreygandhi1990 ▴ 10
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3
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2.9k
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Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 680
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6
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1.4k
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DESeq2:varianceStabilizingTransformation suggested. Results suspicious
deseq2
6.8 years ago jovel_juan ▴ 30
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2
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1.8k
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DESeq2: RNA-Seq time series analysis after removal of batch effect
deseq2 time series remove batch effect
6.8 years ago Nicola • 0
4
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4
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3.1k
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RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 680
2
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1
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1.2k
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tximport: question concerning 'bias corrected counts without an offset' method
tximport deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
8
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4
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3.4k
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edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin edgeR deseq2 normalization rnaseq
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by ▴ 90
0
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1
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1.0k
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Data filtering in DESeq2
deseq2 data filtering
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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5
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872
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DESeq2 overestimates log2Fold Change
deseq2
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
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1
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1.1k
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differentail expression analysis with interaction terms
edger deseq2 interaction design matrix
updated 6.8 years ago by 68k • written 6.8 years ago by ★ 1.5k
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4
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2.2k
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Summary results interpretation in DeSeq2
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
8
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2
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1.4k
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Does IHW use the supplied alpha for the correction calculations?
IHW deseq2
updated 6.8 years ago by ▴ 180 • written 6.8 years ago by ▴ 120
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6
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1.9k
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DESeq2: paired samples + controls
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 20
6
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7
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2.4k
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DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
1
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1
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1.5k
views
design for DEseq2: LRT vs Wald & interactions
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 10
1
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3
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1.6k
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Appropriate design formula for DESeq2 from principles
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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2
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6.8k
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[Resolved] RcppArmadillo pckg ERRORS : non-zero exit status (and so DESeq2 also)
DESEq2 R linux RcppArmadillo
6.8 years ago RS1 • 0
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1
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4.0k
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basemean cut off in DESEQ2
deseq2
6.8 years ago angajalaanusha ▴ 10
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6
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2.1k
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stringasfactor = F changes the output of pheatmap, why?
deseq2 pheatmap
updated 6.8 years ago by ★ 13k • written 6.8 years ago by ▴ 10
2
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3
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926
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Recommendations for normalisation post-deseq2
deseq2 normalization posthoc
6.8 years ago marc.osullivan • 0
1
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1
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1.1k
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Normalized counts from DESeq2 results in similar but not equal total read count?
deseq2 normalization
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
1
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8
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1.1k
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DEseq2 - design help
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
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2
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801
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RESULTS() using contrast=c("condition","A","B"), the results would be A vs B correct?
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 10
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3
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1.1k
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DESeq: Design model for paired design with two treatments
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
4
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6
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4.8k
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DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 21 months ago by • 0 • written 6.8 years ago by ▴ 50
2
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1
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741
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NAs create inaccuracies with BH corrections in deseq2
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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1
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930
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Paired samples in DESeq2
R deseq2 Paired Samples
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
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1
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642
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Script for fold change in DESeq for count data with 2 groups
deseq2 RNAseq
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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1
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634
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Deseq2 two controls in design experiment
Deseq2 RNASeq
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
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9
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17k
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How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 6.8 years ago by • 0
0
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2
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709
views
Error in checkFullRank(modelMatrix) :
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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2
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3.5k
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DESEq2 rownames: NULL
deseq2 R
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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3
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871
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How to specify contrasts in DESeqDataSetFromMatrix
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
3
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1
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540
views
Detect genes that moved up or down over time in the same way in multiple strains, DESeq2
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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1
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2.6k
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Low basemean and extremely high log2FC values, DESeq2
deseq2 interpretation
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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1
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1.2k
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Highly uneven mapping rates and counts between samples
limma normalization deseq2
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 420
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1
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851
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DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2 design
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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2
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2.1k
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DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2 design
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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3
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955
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Comparison of DESeq2 and BNB-R model
DESeq2 BNB-R
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
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3
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823
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How to create 3 way interactions model for Deseq
deseq2
6.8 years ago sharmila.ahmad • 0
0
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0
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760
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diffbind: use of continuous variables
diffbind deseq2
6.8 years ago janani.sundaresan • 0
4,840 results • Page 54 of 97
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Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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.
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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