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Voom
•
reset
3
votes
1
reply
1.9k
views
GLM voom and link Function
limma
voom
updated 10.2 years ago by
Aaron Lun
★ 29k • written 10.2 years ago by
ea1402
▴ 20
1
vote
13
replies
6.9k
views
edgeR vs voom
edger
voom
limma
10.3 years ago
dongamit123
▴ 20
8
votes
2
replies
3.0k
views
limma-voom when testing differential expression of a subset of genes.
limma
voom
differential gene expression
updated 10.3 years ago by
Gordon Smyth
53k • written 10.3 years ago by
ankur.chakravarthy.10
▴ 40
6
votes
5
replies
5.2k
views
voom + removeBatchEffect + gene clustering
voom
limma
clustering
removebatcheffect()
batch effect
updated 10.3 years ago by
Gordon Smyth
53k • written 10.3 years ago by
ale.breschi
▴ 10
21
votes
5
replies
18k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma
voom
updated 10.5 years ago by
Gordon Smyth
53k • written 11.5 years ago by
John Blischak
▴ 190
4
votes
2
replies
4.1k
views
PCA for voom normalized RNAseq data
voom
pca
updated 10.6 years ago by
Aaron Lun
★ 29k • written 10.6 years ago by
Merienne Nicolas
▴ 120
2
votes
6
replies
4.0k
views
voom/limma contrast for comparing one level against base-line
limma
voom
contrast
updated 10.6 years ago by
Steve Lianoglou
★ 13k • written 10.6 years ago by
Stijn van Dongen
▴ 80
3
votes
5
replies
2.6k
views
PCA of voom weight values
limma
voom
rnaseq
updated 10.6 years ago by
Gordon Smyth
53k • written 10.6 years ago by
Lorena Pantano
▴ 140
4
votes
8
replies
4.5k
views
Visualising effects of observation/sample weights in differential expression analysis
limma
voom
sva
edgeR
updated 10.7 years ago by
Matthew Ritchie
▴ 1000 • written 10.7 years ago by
m.fletcher
▴ 20
5
votes
2
replies
3.8k
views
Differences when using voom on a design with or without intercept
limma
voom
linear model
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
Francesco Gatto
▴ 20
25
votes
9
replies
8.3k
views
voom for spectral counts
limma
voom
proteomics
spectral counts
massspectrometry
updated 10.8 years ago by
Gordon Smyth
53k • written 10.8 years ago by
Ben Neely
▴ 40
5
votes
2
replies
7.8k
views
Ballgown vs (voom,edgeR,DESeq,limma)
limma
rnaseq
differential expression
voom
updated 10.8 years ago by
Alyssa Frazee
▴ 210 • written 10.8 years ago by
François Lefebvre
▴ 50
3
votes
3
replies
3.6k
views
Voom without design matrix
limma
voom
10.8 years ago
Ninni Nahm
▴ 50
9
votes
9
replies
6.1k
views
Voom on TCGA data shifts count distributions towards negative values
voom
TCGA
RNAseq
10.9 years ago
paola.ostano
▴ 10
2
votes
7
replies
4.0k
views
limma+voom question for effect across multiple tissues
limma
voom
updated 11.0 years ago by
Aaron Lun
★ 29k • written 11.0 years ago by
artvandelay
▴ 10
4
votes
5
replies
11k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 11.0 years ago by
Steve Lianoglou
★ 13k • written 11.0 years ago by
Peter Crisp
▴ 10
166 results • Page
4 of 4
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Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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