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EdgeR: Explaning dispersion types to newbies
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updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Mr.RB
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Bioconductor-related papers -- special F1000Research collection for Bioc2016
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updated 8.1 years ago by
thomas.ingraham
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Wolfgang Huber
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New Master of Science in Quantitative and Computational Biology at University of Trento, Italy
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updated 7.8 years ago by
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• 0 • written 7.9 years ago by
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Job:
Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
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5.5 years ago
Laurent Gatto
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Bioconductor Community Manager
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Bioconductor
23 months ago • updated 22 months ago
Matthew Ritchie
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Lecturer in Statistics - School of Mathematics and Statistics - University of St Andrews
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21 months ago
Andy Lynch
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Maria Doyle
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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
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…
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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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