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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
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
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
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
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
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
3
votes
4
replies
925
views
How to check whether experimental covariates are confounded with our group of interest?
covariates
microarray
4.5 years ago
english.server
▴ 20
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
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
2
votes
3
replies
821
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
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
0
votes
3
replies
960
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
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
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
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
2
replies
811
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
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
1
reply
838
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
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
0
votes
0
replies
449
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
909
views
How to specify covariates in maSigPro analysis (like limma)
masigpro
covariates
limma
differential expression
time-course
6.5 years ago
veersingh.marwah
• 0
24 results • Page
1 of 1
Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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