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Showing :
makeContrasts
•
reset
3
votes
4
replies
970
views
How to make design matrices or compare contrast in limma
designmatrices
differentialexpression
makeContrasts
limma
model.matrix
17 months ago
mohammedtoufiq91
▴ 10
1
vote
5
replies
870
views
makeContrasts question
makeContrasts
edgeR
updated 2.1 years ago by
Steve Lianoglou
13k • written 2.1 years ago by
HS
▴ 10
1
vote
2
replies
649
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 3.2 years ago by
Gordon Smyth
48k • written 3.2 years ago by
June.
▴ 10
2
votes
2
replies
1.5k
views
makeContrasts for comparing multiple levels of a factor variable to the reference level
diffrential expression
limma
makeContrasts
updated 5.2 years ago by
Gordon Smyth
48k • written 5.2 years ago by
S.Bamopoulos
▴ 10
0
votes
2
replies
769
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq
edgeR
makecontrasts
interactions
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
David R
▴ 70
7
votes
3
replies
4.3k
views
[limma] Define contrasts for model with covariates
limma
model.matrix
makecontrasts
updated 5.2 years ago by
Gordon Smyth
48k • written 5.2 years ago by
enricoferrero
▴ 660
0
votes
1
reply
625
views
DESeq2 : how to make model contrast with multifactors : cond1(env1 versus env2) versus cond2(env1 versus env2) ?
deseq2
makecontrasts
updated 5.8 years ago by
Michael Love
40k • written 5.8 years ago by
samuel.quentin
• 0
3
votes
6
replies
1.8k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix
toptable
makecontrasts
differential gene expression
6.0 years ago
stinehedensted
• 0
2
votes
5
replies
2.0k
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 6.0 years ago by
Gordon Smyth
48k • written 6.1 years ago by
wewolski
▴ 10
1
vote
2
replies
1.1k
views
differentially expressed genes without contrasts
limma
toptable
makecontrasts
contrast matrix
updated 6.2 years ago by
Ryan C. Thompson
7.8k • written 6.2 years ago by
hoe
• 0
0
votes
4
replies
1.5k
views
setting contrast in edgeR for time series data
rnaseq
edger
makecontrasts
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
wangzhang1988
• 0
2
votes
3
replies
1.0k
views
Issues about experiment design
limma
model.matrix
makecontrasts
6.6 years ago • updated 6.5 years ago
TFony
▴ 10
3
votes
4
replies
4.3k
views
multiple comparison using limma
limma
design matrix
makecontrasts
multiple comparisons
6.6 years ago
annabelle.congras
▴ 10
1
vote
6
replies
1.2k
views
edgeR time series DMSO correction
edger
makecontrasts
timecourse
updated 6.9 years ago by
Ryan C. Thompson
7.8k • written 6.9 years ago by
aec
▴ 90
0
votes
7
replies
1.2k
views
why two different makeContrasts have the same results?
edger
makecontrasts
7.3 years ago
xiaoaozqd
• 0
8
votes
12
replies
3.9k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma
microarray
interaction model
multiple factor design
makeContrasts
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
svlachavas
▴ 810
16 results • Page
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Comment: DMRcate design
by
James W. MacDonald
63k
That's what identical context means.
Comment: DMRcate design
by
Jitendra
▴ 10
Thanks James, but I did not understand it clearly. Could I used same Limma design matrix for DMRcate?
Comment: Steps needed to change design (relevel factors) in DESeq2
by
jd774
• 0
Thanks for the example code, would the `"condition_1_vs_2"` and `"condition_2_vs_1"` giving same or different results on DEGs and normalize…
Answer: heatmap.2 - change column & row locations; angle / rotate
by
nehagoyal6397
• 0
Window 10 are comes with the new updates [how to fix connections to wireless displays in windows 10](http://fixwindows10connections.com) ju…
Comment: filtering out lowly expressed genes by groups
by
James W. MacDonald
63k
You might want to filter first though. ``` fun <- function(deseqobj, contvec, cutoff) { lildds <- dds[rowMeans(assays(deseqobj…
Votes
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
Comment: Timely differentially expressed genes
Comment: NPARC package y-variable
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
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