Bioconductor Nanostringdiff

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nanostringdiff nanostring NanoStringDiff

updated 5.9 years ago by James W. MacDonald 65k • written 5.9 years ago by casey.rimland ▴ 150

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1.9k

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NanoStringDiff NanoString nCounter DE analysis

updated 5 months ago by georgersmith • 0 • written 4.7 years ago by lim6432 ▴ 50

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1.5k

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limma edgeR DESeq2 NanoStringDiff

updated 2.6 years ago by James W. MacDonald 65k • written 2.6 years ago by reberya • 0

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1.4k

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NanoStringDiff

updated 3 months ago by pjanas • 0 • written 4.9 years ago by noelleenright ▴ 10

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1.3k

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nanostring NanoStringDiff design and contrast matrix differential gene expression ncounter

6.8 years ago c.kohler • 0

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NanoStringDiff

4.3 years ago stephen.pollo • 0

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966

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Nan NanoStringDiff

2.8 years ago choijamts • 0

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892

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Bioconductor Transcriptomics NanoStringDiff

updated 3.5 years ago by Laurent Gatto 1.6k • written 3.5 years ago by Pedro ▴ 10

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866

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NanoStringDiff GLM Gene expression

updated 4.7 years ago by James W. MacDonald 65k • written 4.7 years ago by Guillaume Robert • 0

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840

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DESeq2 NanoStringDiff limma

11 months ago pg45863 ▴ 10

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816

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NanoStringDiff clusterProfiler fgsea

11 months ago pg45863 ▴ 10

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651

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NanoStringDiff

3.1 years ago YM • 0

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622

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GEOquery MicroarrayData Normalization Microarray NanoStringDiff

updated 14 months ago by James W. MacDonald 65k • written 14 months ago by Aleksandra • 0

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544

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DifferentialExpression NanoStringDiff

2.4 years ago sanrie10 • 0

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509

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NanoStringDiff

updated 16 months ago by James W. MacDonald 65k • written 16 months ago by Paraskevi • 0

15 results • Page 1 of 1

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Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

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 …

Votes

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

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

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0