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block
•
reset
4
votes
14
replies
5.5k
views
Including technical and biological replicates in Limma block analysis?
limma
microarray
block
paired
linear model
9.4 years ago
vas
▴ 40
6
votes
14
replies
3.1k
views
limma with continous covariate depending on gene, 2 block variables, pairing and technical replicates
limma
covariate
block
paired samples
technical replicates
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
eleonoregravier
▴ 70
7
votes
7
replies
8.3k
views
batch effect : comBat or blocking in limma ?
batch effect
combat
limma
block
updated 8.6 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
eleonoregravier
▴ 70
1
vote
6
replies
1.5k
views
DESEQ2 blocking design doesn't match expectation !
deseq2
block
pca
7.8 years ago
akp
• 0
3
votes
5
replies
1.8k
views
Limma contrast matrix question/concern
limma
block
design and contrast matrix
8.9 years ago
choofd
• 0
1
vote
4
replies
2.7k
views
Remove batch effect using individuals as random in the model in Limma
batch effect
Coeficents non estimable
block
random effects
limma design matrix
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
mheydarpour
▴ 10
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 7 months ago by
Gordon Smyth
50k • written 5.2 years ago by
tleona3
• 0
0
votes
3
replies
1.3k
views
About experimental design of RNA-seq
time course
block
batch effect
WGCNA
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
xie186
• 0
4
votes
3
replies
992
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind
block
regression
deseq2
chipseq
updated 3.5 years ago by
Rory Stark
★ 5.2k • written 4.5 years ago by
melnuesch
▴ 10
4
votes
3
replies
2.0k
views
Blocked design and Surrogate Variables Analsysis(SVA)
limma
sva
block
updated 2.2 years ago by
stuartthafass
• 0 • written 9.5 years ago by
kodream
▴ 20
2
votes
2
replies
1.3k
views
limma roast/mroast with patient-matched pre-/post- treatment
limma
roast
mroast
block
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
barbara.shih
• 0
0
votes
1
reply
1.3k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 5.9 years ago by
lhuang7
▴ 50 • written 6.9 years ago by
Simone
▴ 190
0
votes
1
reply
939
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 years ago by
Katherine
• 0
13 results • Page
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Recent ...
Replies
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma
by
James W. MacDonald
65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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