Bioconductor Makecontrasts

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2.2k

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contrast matrix toptable makecontrasts differential gene expression

6.6 years ago stinehedensted • 0

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limma design matrix makecontrasts multiple comparisons

7.2 years ago annabelle.congras ▴ 10

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1.2k

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limma model.matrix makecontrasts

7.2 years ago • updated 7.1 years ago TFony ▴ 10

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edger makecontrasts

7.9 years ago xiaoaozqd • 0

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makeContrasts edgeR

updated 2.7 years ago by Steve Lianoglou ★ 13k • written 2.7 years ago by HS ▴ 10

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729

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deseq2 makecontrasts

updated 6.4 years ago by Michael Love 41k • written 6.4 years ago by samuel.quentin • 0

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limma model.matrix makecontrasts

updated 5.8 years ago by Gordon Smyth 50k • written 5.8 years ago by enricoferrero ▴ 660

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923

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rnaseq edgeR makecontrasts interactions

updated 5.8 years ago by Aaron Lun ★ 28k • written 5.8 years ago by David R ▴ 90

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diffrential expression limma makeContrasts

updated 5.8 years ago by Gordon Smyth 50k • written 5.8 years ago by S.Bamopoulos ▴ 10

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865

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microarray dge matrix makecontrasts limma

updated 3.8 years ago by Gordon Smyth 50k • written 3.8 years ago by June. ▴ 10

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4.2k

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limma microarray interaction model multiple factor design makeContrasts

updated 8.1 years ago by Aaron Lun ★ 28k • written 8.1 years ago by svlachavas ▴ 830

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designmatrices differentialexpression makeContrasts limma model.matrix

2.0 years ago mohammedtoufiq91 ▴ 10

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edger makecontrasts timecourse

updated 7.5 years ago by Ryan C. Thompson ★ 7.9k • written 7.5 years ago by aec ▴ 90

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rnaseq edger makecontrasts

updated 6.9 years ago by Aaron Lun ★ 28k • written 6.9 years ago by wangzhang1988 • 0

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limma toptable makecontrasts contrast matrix

updated 6.8 years ago by Ryan C. Thompson ★ 7.9k • written 6.8 years ago by hoe • 0

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limma contrast missing data lmfit makecontrasts

updated 6.6 years ago by Gordon Smyth 50k • written 6.7 years ago by wewolski ▴ 10

16 results • Page 1 of 1

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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…

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…

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