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makecontrasts
•
reset
3
votes
4
replies
1.3k
views
How to make design matrices or compare contrast in limma
designmatrices
differentialexpression
makeContrasts
limma
model.matrix
2.0 years ago
mohammedtoufiq91
▴ 10
1
vote
5
replies
1.1k
views
makeContrasts question
makeContrasts
edgeR
updated 2.7 years ago by
Steve Lianoglou
★ 13k • written 2.7 years ago by
HS
▴ 10
1
vote
2
replies
864
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
June.
▴ 10
2
votes
2
replies
1.9k
views
makeContrasts for comparing multiple levels of a factor variable to the reference level
diffrential expression
limma
makeContrasts
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
S.Bamopoulos
▴ 10
0
votes
2
replies
923
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq
edgeR
makecontrasts
interactions
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
David R
▴ 90
9
votes
3
replies
5.0k
views
[limma] Define contrasts for model with covariates
limma
model.matrix
makecontrasts
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
enricoferrero
▴ 660
0
votes
1
reply
729
views
DESeq2 : how to make model contrast with multifactors : cond1(env1 versus env2) versus cond2(env1 versus env2) ?
deseq2
makecontrasts
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
samuel.quentin
• 0
3
votes
6
replies
2.2k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix
toptable
makecontrasts
differential gene expression
6.6 years ago
stinehedensted
• 0
2
votes
5
replies
2.3k
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 6.6 years ago by
Gordon Smyth
50k • written 6.7 years ago by
wewolski
▴ 10
1
vote
2
replies
1.3k
views
differentially expressed genes without contrasts
limma
toptable
makecontrasts
contrast matrix
updated 6.8 years ago by
Ryan C. Thompson
★ 7.9k • written 6.8 years ago by
hoe
• 0
0
votes
4
replies
1.6k
views
setting contrast in edgeR for time series data
rnaseq
edger
makecontrasts
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
wangzhang1988
• 0
2
votes
3
replies
1.2k
views
Issues about experiment design
limma
model.matrix
makecontrasts
7.1 years ago
TFony
▴ 10
3
votes
4
replies
4.9k
views
multiple comparison using limma
limma
design matrix
makecontrasts
multiple comparisons
7.2 years ago
annabelle.congras
▴ 10
1
vote
6
replies
1.4k
views
edgeR time series DMSO correction
edger
makecontrasts
timecourse
updated 7.5 years ago by
Ryan C. Thompson
★ 7.9k • written 7.5 years ago by
aec
▴ 90
0
votes
7
replies
1.4k
views
why two different makeContrasts have the same results?
edger
makecontrasts
7.9 years ago
xiaoaozqd
• 0
8
votes
12
replies
4.2k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma
microarray
interaction model
multiple factor design
makeContrasts
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
svlachavas
▴ 830
16 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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