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Covariates
•
reset
3
votes
19
replies
3.5k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.0 years ago
mheydarpour
▴ 10
5
votes
10
replies
1.9k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR
differential expression analysis
covariates
updated 3.7 years ago by
Gordon Smyth
50k • written 3.7 years ago by
Lucy
▴ 60
0
votes
4
replies
2.5k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.4 years ago
j.viana
• 0
3
votes
3
replies
3.1k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.0 years ago
AST
▴ 60
2
votes
3
replies
1.4k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 7.9 years ago by
chris86
▴ 420 • written 7.9 years ago by
TP
• 0
5
votes
7
replies
8.6k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
dmcleanuk
▴ 30
2
votes
3
replies
9.0k
views
DESeq2 model with covariates
deseq2
covariates
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
markus.schulze
• 0
0
votes
1
reply
1.6k
views
DESeq2 biological replicates and RIN values
deseq2
differential gene expression
covariates
rnaseq
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
pmoranlosada
• 0
1
vote
4
replies
20k
views
Adjusting for covariates in paired sample design DESeq2
deseq2
deseq
paired samples
covariates
multiple time points
6.5 years ago
imb
▴ 10
4
votes
3
replies
9.2k
views
How do I extract read counts from DESeq2
deseq2
counts
covariates
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
hechtp
▴ 10
2
votes
4
replies
4.7k
views
Age covariate continuous vs. categorical
deseq2
linear model
covariates
age
design model
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
L_K
• 0
3
votes
4
replies
1.2k
views
Agilent Single-Channel Data: Questions about model statement and model building.
limma
agilent
microarray
covariates
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
CantExitVIM
▴ 10
0
votes
2
replies
1.6k
views
Removing batch effect from gene expression before Limma linear modelling
Limma
differential gene expression
batch effect correction
covariates
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
abelsousa
• 0
5
votes
9
replies
1.6k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
c.bettencourt
• 0
2
votes
2
replies
810
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
Manik Garg
▴ 20
3
votes
4
replies
924
views
How to check whether experimental covariates are confounded with our group of interest?
covariates
microarray
4.5 years ago
english.server
▴ 20
0
votes
1
reply
837
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
rmash
▴ 20
1
vote
2
replies
1.9k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
Mattia
▴ 10
2
votes
3
replies
820
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
ibrahim.akkouh
• 0
0
votes
2
replies
3.1k
views
LIMMA Adjustment for Covariates
limma
covariates
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
trinhpauline
• 0
0
votes
0
replies
448
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
8 months ago
amir
• 0
0
votes
0
replies
1.8k
views
limma: blocking factors and factorial design
limma
differential gene expression
design and contrast matrix
covariates
8.2 years ago
jlerga
• 0
0
votes
0
replies
908
views
How to specify covariates in maSigPro analysis (like limma)
masigpro
covariates
limma
differential expression
time-course
6.5 years ago
veersingh.marwah
• 0
0
votes
3
replies
959
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
dhwani2410
• 0
24 results • Page
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Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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