Showing : DESeq2 • reset
0
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3
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202
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
written 16 days ago by • 0
0
votes
2
replies
255
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
3
votes
6
replies
958
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 6 weeks ago by • 0
0
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1
reply
188
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 5 weeks ago by ★ 5.0k • written 5 weeks ago by • 0
0
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2
replies
1.1k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 6 weeks ago by ★ 4.0k • written 5 months ago by • 0
1
vote
11
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1.9k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 6 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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337
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DESeq2 on non-RNASeq counts data
DESeq2
updated 14 days ago by • 0 • written 4 months ago by • 0
0
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2
replies
343
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 6 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
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0
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149
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 6 weeks ago by ★ 4.0k • written 7 weeks ago by • 0
0
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4
replies
240
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
7 weeks ago • updated 6 weeks ago Denise • 0
0
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2
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259
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Setting up a DESeq2 Design with Paired Data
DESeq2
8 weeks ago Alexander • 0
2
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4
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516
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DESeq2 interactions
DESeq2
updated 9 weeks ago by 43k • written 3 months ago by • 0
3
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14
replies
1.3k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 5 months ago by • 0
0
votes
3
replies
392
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
0
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1
reply
739
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
3
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5
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1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 4 months ago by 68k • written 4 months ago by ▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 4 months ago by 68k • written 6.4 years ago by ▴ 60
0
votes
11
replies
701
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
4 months ago Denise • 0
2
votes
6
replies
641
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
4 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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319
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 4 months ago by ▴ 10
0
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4
replies
965
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
1
vote
2
replies
444
views
Differential expression on the transcript-level
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
3
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13
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2.2k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
4
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8
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2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
5 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago bbao ▴ 10
0
votes
1
reply
565
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 5 months ago by 68k • written 5 months ago by • 0
0
votes
2
replies
1.0k
views
gene detection across experiments
DESeq2 Normalization
6 months ago Mara • 0
5
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11
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3.5k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
1
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5
replies
4.9k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 5 months ago by 43k • written 6 months ago by • 0
1
vote
1
reply
2.2k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 6 months ago by 43k • written 6 months ago by • 0
0
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2
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1.2k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
3
votes
2
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1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
1
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2
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2.7k
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 7 months ago by • 0
3
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1
reply
3.8k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 7 months ago by 43k • written 7 months ago by ▴ 10
0
votes
1
reply
631
views
DESeq2 results
result DESeq2 subsetting
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
456
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
0
votes
1
reply
616
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
7 months ago dudutchy ▴ 10
2
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3
replies
1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 months ago Paulito • 0
4
votes
4
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2.1k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
7 months ago caroline.zanchi ▴ 10
0
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1
reply
454
views
DESeq2 from phyloseq error
DESeq2 phyloseq
7 months ago asafpr • 0
3
votes
1
reply
678
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 7 months ago by 68k • written 7 months ago by • 0
1
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5
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1.5k
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 7 months ago by 68k • written 7 months ago by ▴ 10
9
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3
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3.2k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 7 months ago by 43k • written 8 months ago by ▴ 40
2
votes
4
replies
1.9k
views
Filtering after DESeq
DESeq2 IHW
written 8 months ago by ▴ 10
0
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4
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1.3k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
8 months ago sk • 0
0
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6
replies
1.9k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
8 months ago • updated 7 months ago AMgroup • 0
0
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2
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759
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Design formula for circadian time-course data for vst() function
DESeq2
8 months ago Vishnu • 0
0
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2
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901
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Analyzing TnSeq data with DESeq2
DESeq2
written 8 months ago by • 0
0
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1
reply
1.2k
views
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 8 months ago by 43k • written 9 months ago by • 0
4,842 results • Page 1 of 97
Recent ...
Replies
Comment: Limma-voom sample weights and impact on DEG numbers by A.Barden ▴ 20
Apologies for the late response - thank you for this information, it is very helpful.
Comment: Converting Probe IDs to HGNC symbols by Manav ▴ 10
ah thank u so much
Comment: Guitar R package requires update due to dependency GenomicFeatures by Sean Davis 21k
A great way to communicate such a nice troubleshooting and bug fix hint is to file an issue in github: https://github.com/lzcyzm/Guitar/iss…
Answer: Converting Probe IDs to HGNC symbols by Sean Davis 21k
The brainarray annotations are very confusing, as the IDs in the fData look like affymetrix probe IDs. To clarify, the brainarray project m…
Comment: How to do differential expresion across time serise with edgeR? by Gordon Smyth 53k
If you have fake replicates, then I think my code answers your question about how to run the edgeR time-course analysis. Regarding tutoria…
Votes
Answer: Limma-voom sample weights and impact on DEG numbers
Answer: Limma-voom sample weights and impact on DEG numbers
Answer: Converting Probe IDs to HGNC symbols
Converting Probe IDs to HGNC symbols
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
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