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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 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 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
8.8 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
991
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 2.1 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
▴ 180
0
votes
1
reply
936
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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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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