Showing : outliers • reset
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Differential expression due to extreme outliers in DESeq2
deseq2 outliers
6.3 years ago paul.alto ▴ 50
8
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17
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WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA Sample Size Outliers
updated 8.6 years ago by • 0 • written 9.2 years ago by ▴ 150
8
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2
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
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3
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5.1k
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DESeq2: How to manually perform filtering and outlier detection?
deseq2 filtering outliers count outliers
updated 6.7 years ago by ★ 13k • written 6.7 years ago by ▴ 10
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Deciding on cooks cutoff value DESeq2
deseq2 differential gene expression outliers bioconductor
updated 7.2 years ago by 41k • written 7.2 years ago by ▴ 10
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8
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[DESeq2] Automatic outlier detection and replacement with continuous variables
deseq2 outliers RNAseq differential gene expression
7.1 years ago cajawe • 0
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2.3k
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DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
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Modeling count data that is zero inflated with negative binomial hurdle regression
pscl outliers
updated 9.1 years ago by 21k • written 9.1 years ago by ▴ 30
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Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
deseq2 outliers cooks cooks distance
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
2
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3
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
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9
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1.7k
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DESeq2 influence of 2 samples
deseq2 outliers differential gene expression
updated 7.2 years ago by 41k • written 7.2 years ago by ▴ 10
1
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7
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1.7k
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skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers
updated 5.7 years ago by ★ 7.9k • written 5.7 years ago by ▴ 20
3
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3
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How to define an outlier array from PCA?
microarray PCA outliers sample outliers limma
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 60
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weird behaviour DESeq2 1.18.1
deseq2 outliers version
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 90
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1.4k
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Deseq2 default Cooks distance threshold
Deseq2 outliers cookscutoff
updated 5.7 years ago by 41k • written 5.7 years ago by • 0
0
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4
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1.3k
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significant genes with DESeq2 plenty of outliers and zero counts
zero counts deseq2 odd results outliers
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 90
1
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1
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1.3k
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Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 6.9 years ago by ▴ 420 • written 6.9 years ago by ▴ 30
0
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1
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1.2k
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Handling outliers in Deseq2
outliers deseq2 logfoldchange
6.3 years ago lirongrossmann ▴ 80
1
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2
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1.1k
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Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi normalization outliers dna methylation densityplot
5.7 years ago peter.fransquet • 0
0
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3
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1.0k
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DESeq outlier detection for unbalanced groups
deseq2 deseq outliers
updated 7.7 years ago by 41k • written 7.8 years ago by ▴ 30
1
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2
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1.0k
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rlog vs vst for outlier identification
rlog DESeq2 vst outliers
2.3 years ago Bex • 0
0
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3
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960
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dealing with outliers (deseq2)
maxcooks outliers zero counts DESeq2
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 10
0
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1
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838
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Removal of outliers after library size correction, can I save this to my dds object?
deseq2 outliers
updated 6.1 years ago by 41k • written 6.1 years ago by • 0
0
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2
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716
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Outliers
outliers Deseq2
3.0 years ago nolwenn • 0
0
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1
reply
596
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Which samples to remove from analysis based on Cook's distance outliers plot
DESeq2 cooks outliers
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
25 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
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Install/Switch between multiple versions of R, Rstudio, and Bioconductor
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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