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covariates
•
reset
4
votes
4
replies
1.3k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma
adjustment
voom
removeBatchEffect
covariates
8 months ago
sukeshinik5
▴ 20
0
votes
0
replies
808
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
20 months ago
amir
• 0
5
votes
10
replies
2.8k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR
differential expression analysis
covariates
updated 4.6 years ago by
Gordon Smyth
52k • written 4.6 years ago by
Lucy
▴ 60
2
votes
3
replies
1.1k
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 5.0 years ago by
Kevin Blighe
★ 4.0k • written 5.0 years ago by
ibrahim.akkouh
• 0
0
votes
1
reply
1.2k
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
rmash
▴ 20
0
votes
3
replies
1.2k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
dhwani2410
• 0
3
votes
4
replies
1.2k
views
How to check whether experimental covariates are confounded with our group of interest?
covariates
microarray
5.4 years ago
english.server
▴ 20
2
votes
2
replies
1.0k
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
Manik Garg
▴ 20
5
votes
9
replies
2.1k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
c.bettencourt
• 0
0
votes
2
replies
1.9k
views
Removing batch effect from gene expression before Limma linear modelling
Limma
differential gene expression
batch effect correction
covariates
updated 6.7 years ago by
Gordon Smyth
52k • written 6.7 years ago by
abelsousa
• 0
3
votes
4
replies
1.5k
views
Agilent Single-Channel Data: Questions about model statement and model building.
limma
agilent
microarray
covariates
updated 6.8 years ago by
Gordon Smyth
52k • written 6.8 years ago by
CantExitVIM
▴ 10
2
votes
4
replies
5.9k
views
Age covariate continuous vs. categorical
deseq2
linear model
covariates
age
design model
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
L_K
• 0
0
votes
0
replies
1.1k
views
How to specify covariates in maSigPro analysis (like limma)
masigpro
covariates
limma
differential expression
time-course
7.4 years ago
veersingh.marwah
• 0
1
vote
4
replies
23k
views
Adjusting for covariates in paired sample design DESeq2
deseq2
deseq
paired samples
covariates
multiple time points
7.4 years ago
imb
▴ 10
0
votes
1
reply
1.9k
views
DESeq2 biological replicates and RIN values
deseq2
differential gene expression
covariates
rnaseq
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
pmoranlosada
• 0
2
votes
3
replies
11k
views
DESeq2 model with covariates
deseq2
covariates
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
markus.schulze
• 0
3
votes
19
replies
4.3k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.9 years ago
mheydarpour
▴ 10
0
votes
4
replies
3.0k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
8.3 years ago
j.viana
• 0
5
votes
8
replies
10.0k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 10 months ago by
hortense96
• 0 • written 8.5 years ago by
dmcleanuk
▴ 30
2
votes
3
replies
1.7k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 8.8 years ago by
chris86
▴ 420 • written 8.8 years ago by
TP
• 0
3
votes
3
replies
3.6k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.9 years ago
AST
▴ 60
1
vote
2
replies
2.2k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.9 years ago by
Michael Love
43k • written 8.9 years ago by
Mattia
▴ 10
4
votes
3
replies
11k
views
How do I extract read counts from DESeq2
deseq2
counts
covariates
updated 9.0 years ago by
Michael Love
43k • written 9.0 years ago by
hechtp
▴ 10
0
votes
0
replies
1.9k
views
limma: blocking factors and factorial design
limma
differential gene expression
design and contrast matrix
covariates
9.1 years ago
jlerga
• 0
0
votes
2
replies
3.2k
views
LIMMA Adjustment for Covariates
limma
covariates
updated 9.1 years ago by
Aaron Lun
★ 28k • written 9.1 years ago by
trinhpauline
• 0
25 results • Page
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Comment: Conumee for EPIC and EPICv2 copy number
by
Adam
• 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken
by
shepherl
4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Comment: graper 1.22 Build is Broken
by
shepherl
4.1k
This post does not fit the theme of this forum.
Comment: Unbalanced experiment with multiple samples from each patient.
by
canarias
• 0
Hi Aaron, I'm faced with an analysis that has basically the same problem as OP had, but is probably even more unbalanced: In most cases, I…
Comment: Gene Set Enrichment Analysis in Bioconductor course
by
info
▴ 10
If you are interested in Gene Set Enrichment Analysis in R, you can still join us next week for this 4-day Physalia course on GSEA in R and…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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