Showing : Outliers • reset
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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
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3
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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
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rlog vs vst for outlier identification
rlog DESeq2 vst outliers
2.3 years ago Bex • 0
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2
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6.8k
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
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Outliers
outliers Deseq2
3.0 years ago nolwenn • 0
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2.0k
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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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1.9k
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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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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
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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
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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
5.8 years ago peter.fransquet • 0
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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
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6
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1.5k
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weird behaviour DESeq2 1.18.1
deseq2 outliers version
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 90
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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
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1.2k
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Handling outliers in Deseq2
outliers deseq2 logfoldchange
6.3 years ago lirongrossmann ▴ 80
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10
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17k
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Differential expression due to extreme outliers in DESeq2
deseq2 outliers
6.4 years ago • updated 6.3 years ago paul.alto ▴ 50
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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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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
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
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8
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3.1k
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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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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
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7
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3.6k
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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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3
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1.0k
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DESeq outlier detection for unbalanced groups
deseq2 deseq outliers
updated 7.8 years ago by 41k • written 7.8 years ago by ▴ 30
3
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3
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1.6k
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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
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
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2.2k
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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
25 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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