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covariates
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0
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481
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
9 months ago
amir
• 0
5
votes
10
replies
2.0k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR
differential expression analysis
covariates
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
Lucy
▴ 60
2
votes
3
replies
840
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
ibrahim.akkouh
• 0
0
votes
1
reply
872
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
3
replies
978
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
dhwani2410
• 0
3
votes
4
replies
949
views
How to check whether experimental covariates are confounded with our group of interest?
covariates
microarray
4.6 years ago
english.server
▴ 20
2
votes
2
replies
824
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Manik Garg
▴ 20
5
votes
9
replies
1.7k
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
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 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
abelsousa
• 0
3
votes
4
replies
1.2k
views
Agilent Single-Channel Data: Questions about model statement and model building.
limma
agilent
microarray
covariates
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
CantExitVIM
▴ 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
0
votes
0
replies
929
views
How to specify covariates in maSigPro analysis (like limma)
masigpro
covariates
limma
differential expression
time-course
6.6 years ago
veersingh.marwah
• 0
1
vote
4
replies
20k
views
Adjusting for covariates in paired sample design DESeq2
deseq2
deseq
paired samples
covariates
multiple time points
6.6 years ago
imb
▴ 10
0
votes
1
reply
1.6k
views
DESeq2 biological replicates and RIN values
deseq2
differential gene expression
covariates
rnaseq
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
pmoranlosada
• 0
2
votes
3
replies
9.1k
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
3
votes
19
replies
3.6k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.1 years ago
mheydarpour
▴ 10
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
5
votes
7
replies
8.7k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
dmcleanuk
▴ 30
2
votes
3
replies
1.4k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 8.0 years ago by
chris86
▴ 420 • written 8.0 years ago by
TP
• 0
3
votes
3
replies
3.2k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.1 years ago • updated 8.0 years ago
AST
▴ 60
1
vote
2
replies
1.9k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
Mattia
▴ 10
4
votes
3
replies
9.3k
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
0
replies
1.8k
views
limma: blocking factors and factorial design
limma
differential gene expression
design and contrast matrix
covariates
8.3 years ago
jlerga
• 0
0
votes
2
replies
3.1k
views
LIMMA Adjustment for Covariates
limma
covariates
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
trinhpauline
• 0
24 results • Page
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Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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