Bioconductor Quantsmooth

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quantsmooth

updated 9.6 years ago by Jan Oosting ▴ 20 • written 9.6 years ago by bob.stephens.2005 • 0

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quantsmooth quantsmooth

12.6 years ago Srinivas Srikanth ▴ 70

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ideogram quantsmooth GenomeGraphs ideogram quantsmooth GenomeGraphs

12.8 years ago Pete Shepard ▴ 240

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Clustering annotate quantsmooth Clustering annotate quantsmooth

updated 13.0 years ago by Oosting, J. PATH ▴ 550 • written 13.0 years ago by Nandini B ▴ 30

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.5 years ago by Matt Ritchie ▴ 460 • written 16.5 years ago by Elizabeth McClellan ▴ 10

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935

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Biobase annotate affy affyio beadarray quantsmooth beadarraySNP lumi Biobase annotate

16.7 years ago Johnstone, Alice ▴ 410

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1.2k

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.7 years ago by Mark Dunning ▴ 320 • written 16.7 years ago by Krys Kelly ▴ 270

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1.4k

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.7 years ago by Mark Dunning ▴ 320 • written 16.7 years ago by Johnstone, Alice ▴ 410

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1.5k

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.8 years ago by Mike Smith ▴ 40 • written 16.8 years ago by Krys Kelly ▴ 270

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1.2k

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Microarray Annotation geneplotter affy affyio beadarray quantsmooth beadarraySNP affy

updated 16.8 years ago by Matt Ritchie ▴ 460 • written 16.8 years ago by Keith James ▴ 10

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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