Bioconductor Makecontrasts

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designmatrices differentialexpression makeContrasts limma model.matrix

2.7 years ago mohammedtoufiq91 ▴ 10

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makeContrasts edgeR

updated 3.4 years ago by Steve Lianoglou ★ 13k • written 3.4 years ago by Lina ▴ 10

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microarray dge matrix makecontrasts limma

updated 4.5 years ago by Gordon Smyth 52k • written 4.5 years ago by June. ▴ 10

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diffrential expression limma makeContrasts

updated 6.5 years ago by Gordon Smyth 52k • written 6.5 years ago by S.Bamopoulos ▴ 10

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rnaseq edgeR makecontrasts interactions

updated 6.5 years ago by Aaron Lun ★ 28k • written 6.5 years ago by David R ▴ 90

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limma model.matrix makecontrasts

updated 6.5 years ago by Gordon Smyth 52k • written 6.5 years ago by enricoferrero ▴ 660

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858

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deseq2 makecontrasts

updated 7.1 years ago by Michael Love 43k • written 7.1 years ago by samuel.quentin • 0

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contrast matrix toptable makecontrasts differential gene expression

7.3 years ago • updated 7.2 years ago stinehedensted • 0

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limma contrast missing data lmfit makecontrasts

updated 7.3 years ago by Gordon Smyth 52k • written 7.4 years ago by wewolski ▴ 10

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limma toptable makecontrasts contrast matrix

updated 7.5 years ago by Ryan C. Thompson ★ 7.9k • written 7.5 years ago by hoe • 0

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rnaseq edger makecontrasts

updated 7.6 years ago by Aaron Lun ★ 28k • written 7.6 years ago by wangzhang1988 • 0

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limma model.matrix makecontrasts

7.8 years ago TFony ▴ 10

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limma design matrix makecontrasts multiple comparisons

7.9 years ago annabelle.congras ▴ 10

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edger makecontrasts timecourse

updated 8.1 years ago by Ryan C. Thompson ★ 7.9k • written 8.1 years ago by aec ▴ 90

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edger makecontrasts

8.6 years ago xiaoaozqd • 0

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limma microarray interaction model multiple factor design makeContrasts

updated 8.8 years ago by Aaron Lun ★ 28k • written 8.8 years ago by svlachavas ▴ 840

16 results • Page 1 of 1

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Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

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A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

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