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 ★ 4.1k • written 14 months ago by • 0
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3
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984
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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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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
8
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2
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6.9k
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
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2
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736
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Outliers
outliers Deseq2
3.1 years ago nolwenn • 0
7
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8
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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 5.8 years ago by 41k • written 5.8 years ago by • 0
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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
5.8 years ago peter.fransquet • 0
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850
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Removal of outliers after library size correction, can I save this to my dds object?
deseq2 outliers
updated 6.2 years ago by 41k • written 6.2 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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1.4k
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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 paul.alto ▴ 50
1
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3
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5.2k
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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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4
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2.4k
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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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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
0
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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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1.1k
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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 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 60
8
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17
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14k
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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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0
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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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Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by James W. MacDonald 65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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