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Covariates
•
reset
1
vote
4
replies
466
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
5 days ago • updated 4 days ago
sukeshinik5
• 0
0
votes
0
replies
544
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
12 months ago
amir
• 0
5
votes
10
replies
2.2k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR
differential expression analysis
covariates
updated 4.0 years ago by
Gordon Smyth
51k • written 4.0 years ago by
Lucy
▴ 60
2
votes
3
replies
891
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 4.3 years ago by
Kevin Blighe
★ 3.9k • written 4.3 years ago by
ibrahim.akkouh
• 0
0
votes
1
reply
934
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
rmash
▴ 20
0
votes
3
replies
1.0k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
dhwani2410
• 0
3
votes
4
replies
1.0k
views
How to check whether experimental covariates are confounded with our group of interest?
covariates
microarray
4.8 years ago • updated 4.7 years ago
english.server
▴ 20
2
votes
2
replies
869
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
Manik Garg
▴ 20
5
votes
9
replies
1.8k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
c.bettencourt
• 0
0
votes
2
replies
1.7k
views
Removing batch effect from gene expression before Limma linear modelling
Limma
differential gene expression
batch effect correction
covariates
updated 6.1 years ago by
Gordon Smyth
51k • written 6.1 years ago by
abelsousa
• 0
3
votes
4
replies
1.3k
views
Agilent Single-Channel Data: Questions about model statement and model building.
limma
agilent
microarray
covariates
updated 6.2 years ago by
Gordon Smyth
51k • written 6.2 years ago by
CantExitVIM
▴ 10
2
votes
4
replies
5.0k
views
Age covariate continuous vs. categorical
deseq2
linear model
covariates
age
design model
updated 6.4 years ago by
Michael Love
42k • written 6.4 years ago by
L_K
• 0
0
votes
0
replies
963
views
How to specify covariates in maSigPro analysis (like limma)
masigpro
covariates
limma
differential expression
time-course
6.7 years ago
veersingh.marwah
• 0
1
vote
4
replies
21k
views
Adjusting for covariates in paired sample design DESeq2
deseq2
deseq
paired samples
covariates
multiple time points
6.8 years ago
imb
▴ 10
0
votes
1
reply
1.7k
views
DESeq2 biological replicates and RIN values
deseq2
differential gene expression
covariates
rnaseq
updated 6.8 years ago by
Michael Love
42k • written 6.8 years ago by
pmoranlosada
• 0
2
votes
3
replies
9.5k
views
DESeq2 model with covariates
deseq2
covariates
updated 6.9 years ago by
Michael Love
42k • written 6.9 years ago by
markus.schulze
• 0
3
votes
19
replies
3.7k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.3 years ago
mheydarpour
▴ 10
0
votes
4
replies
2.6k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.6 years ago
j.viana
• 0
5
votes
8
replies
9.0k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 9 weeks ago by
hortense96
• 0 • written 7.9 years ago by
dmcleanuk
▴ 30
2
votes
3
replies
1.5k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 8.2 years ago by
chris86
▴ 420 • written 8.2 years ago by
TP
• 0
3
votes
3
replies
3.3k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.2 years ago
AST
▴ 60
1
vote
2
replies
1.9k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.3 years ago by
Michael Love
42k • written 8.3 years ago by
Mattia
▴ 10
4
votes
3
replies
9.7k
views
How do I extract read counts from DESeq2
deseq2
counts
covariates
updated 8.3 years ago by
Michael Love
42k • written 8.3 years ago by
hechtp
▴ 10
0
votes
0
replies
1.8k
views
limma: blocking factors and factorial design
limma
differential gene expression
design and contrast matrix
covariates
8.4 years ago
jlerga
• 0
0
votes
2
replies
3.1k
views
LIMMA Adjustment for Covariates
limma
covariates
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
trinhpauline
• 0
25 results • Page
1 of 1
Recent ...
Replies
Answer: Ranking the GSEA Results
by
Michael Love
42k
Some posts on this topic: https://www.google.com/search?q=site%3Asupport.bioconductor.org+GSEA+ranking+DESeq2
Answer: Advice on appropriateness of an offset in glmGamPoi/edgeR
by
Gordon Smyth
51k
edgeR allows observation specific offsets (as already pointed out), although I am not confident that would be a reliable solution to your p…
Comment: Research Project - Expanding search funtionality on the GEO database
by
gallantk5
• 0
Thank you I will take a look at those !
Comment: Research Project - Expanding search funtionality on the GEO database
by
gallantk5
• 0
I will send you an email and talk to my advisor about setting up a meeting. Thank you !
Comment: Research Project - Expanding search funtionality on the GEO database
by
Sean Davis
21k
You can use the Bioconductor Annotation packages for the Affymetrix chips of interest. - https://bioconductor.org/packages/release/BiocVie…
Votes
Answer: DESeq2 time course using fitted splines
Answer: DESeq2 time course using fitted splines
Comment: Difference between enrichGO results and Enrichr website results
Answer: Struggling to convert a large list of non-model genes into human orthologs, any
A: makeContrasts from limma overides "i" as a varible
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