Bioconductor PCAtools

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DESeq2 RSTUDIO PCAtools

updated 4 hours ago by swbarnes2 ★ 1.3k • written 1 day ago by Aaliya • 0

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edgeR PCAtools

updated 25 days ago by Gordon Smyth 50k • written 27 days ago by Fabian • 0

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DESeq2 PCAtools

6 hours ago Aaliya • 0

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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…

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C: null model and DEXSeqDataSet object in DEXSEQ

Answer: Interpret plot from DiffBind

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Supporter to JKim • 0