Showing : Deseq2 • reset
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 5 hours ago by 68k • written 8 hours ago by • 0
3
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5
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382
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 7 hours ago by 68k • written 6 days ago by ▴ 200
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0
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56
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Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
8 days ago KS • 0
17
votes
45
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12k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 7 days ago by 68k • written 6.1 years ago by ▴ 60
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0
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64
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DESeq2 on non-RNASeq counts data
DESeq2
12 days ago vs • 0
1
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9
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589
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
15 days ago • updated 11 days ago Raya • 0
0
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11
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356
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
17 days ago • updated 12 days ago Denise • 0
2
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6
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329
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
19 days ago • updated 18 days ago richardallenfriedmanbrooklyn ▴ 30
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3
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142
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 19 days ago by ▴ 10
3
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12
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623
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
updated 14 days ago by 43k • written 4 weeks ago by • 0
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4
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742
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 29 days ago by 43k • written 6 weeks ago by • 0
1
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2
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295
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Differential expression on the transcript-level
DESeq2
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
3
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11
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1.8k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 11 months ago by • 0
4
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8
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1.7k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 weeks ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.3k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 weeks ago bbao ▴ 10
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2
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869
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
0
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1
reply
407
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
0
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2
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877
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gene detection across experiments
DESeq2 Normalization
9 weeks ago Mara • 0
5
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11
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2.9k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 4 months ago by ▴ 10
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5
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3.6k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 5 weeks ago by 43k • written 12 weeks ago by • 0
1
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1
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2.1k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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2
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1.1k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
3
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2
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1.3k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 12 weeks ago by ▴ 20
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2
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2.5k
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 12 weeks ago by • 0
3
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1
reply
3.7k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 12 weeks ago by 43k • written 3 months ago by ▴ 10
0
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1
reply
432
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DESeq2 results
result DESeq2 subsetting
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
0
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1
reply
349
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
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435
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 3 months ago by 43k • written 3 months ago by • 0
3
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2
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2.0k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
3 months ago dudutchy ▴ 10
2
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3
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1.2k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
3 months ago Paulito • 0
4
votes
4
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1.9k
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
3 months ago caroline.zanchi ▴ 10
0
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1
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351
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DESeq2 from phyloseq error
DESeq2 phyloseq
3 months ago asafpr • 0
3
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1
reply
531
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 3 months ago by 68k • written 3 months ago by • 0
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5
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1.2k
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 3 months ago by 68k • written 3 months ago by ▴ 10
8
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3
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2.9k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 3 months ago by 43k • written 4 months ago by ▴ 40
2
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4
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1.6k
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Filtering after DESeq
DESeq2 IHW
written 4 months ago by ▴ 10
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4
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1.1k
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DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
4 months ago • updated 3 months ago sk • 0
0
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6
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1.6k
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Discrepancies in normalised count data vs unnormalised
DESeq2
4 months ago • updated 3 months ago AMgroup • 0
0
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2
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619
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Design formula for circadian time-course data for vst() function
DESeq2
4 months ago Vishnu • 0
0
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2
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758
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Analyzing TnSeq data with DESeq2
DESeq2
written 4 months ago by • 0
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1
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1.1k
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How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 4 months ago by 43k • written 5 months ago by • 0
0
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2
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645
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Differing results with DESeq2
DESeq2
updated 4 months ago by • 0 • written 5 months ago by • 0
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2
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527
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RNA Seq using Lrt
DESeq2
4 months ago Rob • 0
0
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3
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930
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Log2foldchange strange behavior
DESeq2
updated 4 months ago by ★ 4.9k • written 4 months ago by • 0
0
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1
reply
816
views
WGCNA
WGCNA DESeq2
updated 4 months ago by ★ 4.9k • written 4 months ago by • 0
0
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1
reply
995
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Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 4 months ago by ★ 1.4k • written 4 months ago by ▴ 20
1
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1
reply
1.3k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 4 months ago by 4.2k • written 4 months ago by • 0
0
votes
1
reply
441
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 4 months ago by 68k • written 4 months ago by ▴ 30
1
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3
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973
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DESeq - help with pair wise comparisons
DESeq2
4 months ago bd2000 ▴ 30
1
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8
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2.8k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
5 months ago • updated 4 months ago ktz • 0
4,834 results • Page 1 of 97
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Replies
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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