Showing : DESEq2 • reset
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
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4
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878
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
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10
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1.7k
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DESeq2 filtering vs edgeR filtering
DESeq2
written 20 months ago by • 0
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2
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3.1k
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
20 months ago kcarey • 0
1
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1
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589
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i'm not getting any differentially expressed genes.
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
2
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1
reply
814
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
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1
reply
520
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Perform PCA for sample clustering using DESeq2
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
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3
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1.0k
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
0
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2
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949
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DESeq2: Comparing A Knockout to a Strain
DESeq2
21 months ago • updated 20 months ago Viktor Thiel • 0
0
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1
reply
844
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DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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8
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1.5k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
21 months ago michelafrancesconi8 • 0
0
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1
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666
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Unusually large fold-changes in Deseq2 results
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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4
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913
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DESeq2 Replicates
DESeq2 RNASeq
21 months ago kcarey • 0
2
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6
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1.0k
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Factor vs Character in design
DESeq2
21 months ago James Aiden • 0
1
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3
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1.0k
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Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
21 months ago I-Hsuan Lin ▴ 10
4
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7
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1.8k
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weird volcano plot
DESeq2
updated 21 months ago by • 0 • written 2.1 years ago by ▴ 10
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1
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731
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DEseq2 dispersion plot
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
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3
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1.1k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 21 months ago by ★ 1.4k • written 21 months ago by ▴ 10
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2
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1.1k
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Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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3
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943
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 21 months ago by 68k • written 21 months ago by ▴ 10
0
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1
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698
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 21 months ago by 68k • written 21 months ago by • 0
1
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4
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997
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Further clarification of unbalanced group sizes DESeq2
DESeq2
21 months ago hmillike • 0
0
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1
reply
477
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few significant genes from DESeq2 analysis
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
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4
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1.5k
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DEseq2 coefficient
DESeq2 coefficient
21 months ago • updated 19 months ago JKim • 0
3
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5
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1.8k
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
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1
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744
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
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2
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828
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locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
21 months ago Hope ▴ 10
1
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2
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852
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evaluate the variable importance on genes
DESeq2 deseq
21 months ago Meme • 0
0
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3
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831
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library sizes differ extremely after dds
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
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4
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1.5k
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Comparing gene expression across three tissue types to identify any difference.
DESeq2
21 months ago James Aiden • 0
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13
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1.9k
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Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 21 months ago by 43k • written 21 months ago by • 0
1
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5
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983
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vst transformation and zero counts
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 740
1
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12
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2.7k
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
21 months ago paria.alipour • 0
0
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3
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1.4k
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utf-8 codec can't decode byte 0xd5
importr DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
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484
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Problems with filtering DESeq Results (log2fold change)
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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3
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1.2k
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DESeq2: Adjust for treatment effect patient vs control
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
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1.9k
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Pseudobulk-DESeq2 analyze multiple cell types at once?
pseudobulk DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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7
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1.3k
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DESeq filtering specific to contrasts
DESeq2
updated 19 months ago by 43k • written 21 months ago by • 0
0
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2
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849
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help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
21 months ago ccshao ▴ 70
0
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1
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666
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Double batch effect (Individuals nested within blocks in DESeq2)
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
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2
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960
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DESeq2 issue: can't create DESeq2 object
DESeq2 RBioinf
21 months ago Magdalena • 0
0
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1
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455
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Inconsistency in DESeq2 Log fold change
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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3
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761
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DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2 dese
written 21 months ago by • 0
0
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5
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1.2k
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DESEQ2 Repeated Measures-like design error help
DESeq2
updated 21 months ago by 43k • written 21 months ago by ▴ 10
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3
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1.1k
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DESeq2 interaction terms RIPseq analysis
DESeq2 RIPSeq
updated 21 months ago by 43k • written 22 months ago by • 0
2
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2
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1.7k
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
22 months ago jackafiore • 0
4
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2
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2.7k
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How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 22 months ago by ▴ 40 • written 22 months ago by • 0
1
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2
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2.4k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.6 years ago by • 0
0
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2
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729
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
22 months ago Lily Cheang ▴ 10
0
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4
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872
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DESeq2 nomalize value
DESeq2
22 months ago 史哲 • 0
4,839 results • Page 7 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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