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makeContrasts
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3
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4
replies
1.7k
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How to make design matrices or compare contrast in limma
designmatrices
differentialexpression
makeContrasts
limma
model.matrix
2.8 years ago
mohammedtoufiq91
▴ 10
1
vote
5
replies
1.5k
views
makeContrasts question
makeContrasts
edgeR
updated 3.5 years ago by
Steve Lianoglou
★ 13k • written 3.5 years ago by
Lina
▴ 10
1
vote
2
replies
1.1k
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 4.6 years ago by
Gordon Smyth
52k • written 4.6 years ago by
June.
▴ 10
2
votes
2
replies
2.4k
views
makeContrasts for comparing multiple levels of a factor variable to the reference level
diffrential expression
limma
makeContrasts
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
S.Bamopoulos
▴ 10
0
votes
2
replies
1.1k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq
edgeR
makecontrasts
interactions
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
David R
▴ 90
9
votes
3
replies
5.8k
views
[limma] Define contrasts for model with covariates
limma
model.matrix
makecontrasts
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
enricoferrero
▴ 680
0
votes
1
reply
874
views
DESeq2 : how to make model contrast with multifactors : cond1(env1 versus env2) versus cond2(env1 versus env2) ?
deseq2
makecontrasts
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
samuel.quentin
• 0
3
votes
6
replies
2.6k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix
toptable
makecontrasts
differential gene expression
7.4 years ago
stinehedensted
• 0
2
votes
5
replies
2.7k
views
Why does limma contrast.fit produces NA's for all contrast although missing data only in one condition?
limma
contrast
missing data
lmfit
makecontrasts
updated 7.4 years ago by
Gordon Smyth
52k • written 7.5 years ago by
wewolski
▴ 10
1
vote
2
replies
1.5k
views
differentially expressed genes without contrasts
limma
toptable
makecontrasts
contrast matrix
updated 7.6 years ago by
Ryan C. Thompson
★ 7.9k • written 7.6 years ago by
hoe
• 0
0
votes
4
replies
1.9k
views
setting contrast in edgeR for time series data
rnaseq
edger
makecontrasts
updated 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
wangzhang1988
• 0
2
votes
3
replies
1.4k
views
Issues about experiment design
limma
model.matrix
makecontrasts
8.0 years ago • updated 7.9 years ago
TFony
▴ 10
3
votes
4
replies
5.7k
views
multiple comparison using limma
limma
design matrix
makecontrasts
multiple comparisons
8.0 years ago
annabelle.congras
▴ 10
1
vote
6
replies
1.7k
views
edgeR time series DMSO correction
edger
makecontrasts
timecourse
updated 8.3 years ago by
Ryan C. Thompson
★ 7.9k • written 8.3 years ago by
aec
▴ 90
0
votes
7
replies
1.6k
views
why two different makeContrasts have the same results?
edger
makecontrasts
8.7 years ago
xiaoaozqd
• 0
8
votes
12
replies
4.6k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma
microarray
interaction model
multiple factor design
makeContrasts
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
svlachavas
▴ 840
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Comment: WGCNA coupled with differential expression analysis: question about baseline mod
by
hetaf16210
• 0
@[slope][1] If feasible, consider conducting both analyses. Start with a pooled analysis to identify broad patterns, then conduct separate …
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
980linnet
• 0
Stuck on DESeq2 with alpha=.05 for padj cutoff. Can't seem to get the differential expression analysis to stick the landing - it's like try…
Comment: internal error in trio library when trying to use lfmm() in LEA package
by
PW
• 0
>ERROR: unable to open file D://anole_geno.snmf/K1/run1/anole_geno_r1.1.Q. Please, check that the name of the file you provided is correct.…
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
Guilherme
• 0
Thank you for your answer So the proper way to conduct the analysis is to put the filters in the results() function and later filter the da…
Comment: DiffBind - observation that the default union overlap is actually a gap of 1 bp
by
Ian D.
▴ 70
Please can you comment on this @rory.
Votes
A: how to extract Granges not overlapping with other ganges?
DESeq2 1.20.0 lfcshrink function
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
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