Bioconductor MakeContrasts

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designmatrices differentialexpression makeContrasts limma model.matrix

2.1 years ago mohammedtoufiq91 ▴ 10

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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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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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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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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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limma model.matrix makecontrasts

updated 5.9 years ago by Gordon Smyth 50k • written 5.9 years ago by enricoferrero ▴ 660

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732

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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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contrast matrix toptable makecontrasts differential gene expression

6.6 years ago stinehedensted • 0

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limma contrast missing data lmfit makecontrasts

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

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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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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 model.matrix makecontrasts

7.2 years ago TFony ▴ 10

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limma design matrix makecontrasts multiple comparisons

7.2 years ago annabelle.congras ▴ 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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edger makecontrasts

7.9 years ago xiaoaozqd • 0

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limma microarray interaction model multiple factor design makeContrasts

updated 8.2 years ago by Aaron Lun ★ 28k • written 8.2 years ago by svlachavas ▴ 830

16 results • Page 1 of 1

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Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k

I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …

Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

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Answer: DEseq2 coefficient

SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

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Scholar to Rory Stark ★ 5.2k

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