Bioconductor Outlier

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6.5k

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deseq2 rnaseq PCA hierarchical clustering outlier

7.4 years ago wd ▴ 30

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4.5k

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DESeq2 outlier RNASeq

updated 9.4 years ago by Michael Love 41k • written 9.4 years ago by kenneth.daily • 0

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1.9k

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RNAseq DESeq2 outlier counts DE analysis

updated 3.9 years ago by Kevin Blighe ★ 3.9k • written 3.9 years ago by DcL-A • 0

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1.5k

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rnaseq outlier statistics batch effect

updated 7.9 years ago by Gordon Smyth 50k • written 7.9 years ago by grastalt27 • 0

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1.3k

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arrayQualityMetrics Microarray Outlier

updated 8.4 years ago by Wolfgang Huber ★ 13k • written 8.4 years ago by horcsct ▴ 10

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1.2k

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DESeq2 RNAseq outlier

updated 14 months ago by ATpoint ★ 4.0k • written 14 months ago by James • 0

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730

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deseq2 outlier normalization removal

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by knholm • 0

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437

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Outlier

updated 13 months ago by ATpoint ★ 4.0k • written 13 months ago by sanchita.bhattacharya • 0

8 results • Page 1 of 1

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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…

Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k

IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…

Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…

Votes

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Answer: How to retrieve gene ontology GO class from gene list?

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Supporter to JKim • 0