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Covariates
•
reset
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
5
votes
10
replies
2.1k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR
differential expression analysis
covariates
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
Lucy
▴ 60
0
votes
4
replies
2.6k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.5 years ago
j.viana
• 0
3
votes
3
replies
3.2k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.1 years ago
AST
▴ 60
2
votes
3
replies
1.5k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 8.0 years ago by
chris86
▴ 420 • written 8.1 years ago by
TP
• 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 25 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
2
votes
3
replies
9.3k
views
DESeq2 model with covariates
deseq2
covariates
updated 6.8 years ago by
Michael Love
42k • written 6.8 years ago by
markus.schulze
• 0
0
votes
1
reply
1.7k
views
DESeq2 biological replicates and RIN values
deseq2
differential gene expression
covariates
rnaseq
updated 6.7 years ago by
Michael Love
42k • written 6.7 years ago by
pmoranlosada
• 0
1
vote
4
replies
21k
views
Adjusting for covariates in paired sample design DESeq2
deseq2
deseq
paired samples
covariates
multiple time points
6.6 years ago
imb
▴ 10
4
votes
3
replies
9.5k
views
How do I extract read counts from DESeq2
deseq2
counts
covariates
updated 8.2 years ago by
Michael Love
42k • written 8.2 years ago by
hechtp
▴ 10
2
votes
4
replies
4.9k
views
Age covariate continuous vs. categorical
deseq2
linear model
covariates
age
design model
updated 6.3 years ago by
Michael Love
42k • written 6.3 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 6.0 years ago by
Gordon Smyth
50k • written 6.0 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 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
abelsousa
• 0
5
votes
9
replies
1.7k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
c.bettencourt
• 0
2
votes
2
replies
845
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
42k • written 4.9 years ago by
Manik Garg
▴ 20
3
votes
4
replies
978
views
How to check whether experimental covariates are confounded with our group of interest?
covariates
microarray
4.6 years ago
english.server
▴ 20
0
votes
1
reply
904
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
rmash
▴ 20
1
vote
2
replies
1.9k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.2 years ago by
Michael Love
42k • written 8.2 years ago by
Mattia
▴ 10
2
votes
3
replies
865
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 4.2 years ago by
Kevin Blighe
★ 3.9k • written 4.2 years ago by
ibrahim.akkouh
• 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
0
votes
0
replies
509
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
10 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
8.3 years ago
jlerga
• 0
0
votes
0
replies
947
views
How to specify covariates in maSigPro analysis (like limma)
masigpro
covariates
limma
differential expression
time-course
6.6 years ago
veersingh.marwah
• 0
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 4.6 years ago by
Martin Morgan
25k • written 4.6 years ago by
dhwani2410
• 0
24 results • Page
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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