Bioconductor MakeContrasts

Showing : makeContrasts • reset

votes

replies

2.2k

views

contrast matrix toptable makecontrasts differential gene expression

6.6 years ago stinehedensted • 0

votes

replies

4.9k

views

limma design matrix makecontrasts multiple comparisons

7.3 years ago • updated 7.2 years ago annabelle.congras ▴ 10

votes

replies

1.2k

views

limma model.matrix makecontrasts

7.2 years ago TFony ▴ 10

votes

replies

1.4k

views

edger makecontrasts

7.9 years ago xiaoaozqd • 0

vote

replies

1.1k

views

makeContrasts edgeR

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

votes

734

views

deseq2 makecontrasts

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

votes

replies

5.0k

views

limma model.matrix makecontrasts

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

votes

replies

932

views

rnaseq edgeR makecontrasts interactions

updated 5.9 years ago by Aaron Lun ★ 28k • written 5.9 years ago by David R ▴ 90

votes

replies

1.9k

views

diffrential expression limma makeContrasts

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

vote

replies

876

views

microarray dge matrix makecontrasts limma

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

votes

replies

4.2k

views

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

votes

replies

1.4k

views

designmatrices differentialexpression makeContrasts limma model.matrix

2.1 years ago mohammedtoufiq91 ▴ 10

vote

replies

1.4k

views

edger makecontrasts timecourse

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

votes

replies

1.6k

views

rnaseq edger makecontrasts

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

vote

replies

1.3k

views

limma toptable makecontrasts contrast matrix

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

votes

replies

2.4k

views

limma contrast missing data lmfit makecontrasts

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

16 results • Page 1 of 1

Recent ...

Replies

Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

Awards • All