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News:
Bug in ChAMP package champ.SVD() function
champ
methylation
450k
SVD
EPIC
News
7.7 years ago
Yuan Tian
▴ 90
4
votes
5
replies
2.8k
views
SVA and proportion of variance explained
sva
svd
explained variance
pca
updated 7.5 years ago by
Jeff Leek
▴ 650 • written 7.5 years ago by
Mattia
▴ 10
0
votes
2
replies
1.6k
views
Some terms in EPIC Methylation Analysis
ChAMP
SVD
Array
Slide
Sample Plate
updated 5.6 years ago by
Yuan Tian
▴ 280 • written 5.6 years ago by
yuabrahamliu
• 0
0
votes
2
replies
753
views
error in champ.SVD
svd
methylation
champ
updated 12 months ago by
shepherl
3.9k • written 12 months ago by
Giulia
• 0
0
votes
0
replies
361
views
Distance between columns vs distance between rows and SVD
distance
svd
15 months ago
Lenny186
• 0
5 results • Page
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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…
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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
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