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Covariates
•
reset
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
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
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
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 1 day ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
2
votes
4
replies
4.8k
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
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
3
votes
3
replies
3.2k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.1 years ago
AST
▴ 60
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
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
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
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
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
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
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
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
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
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
3
replies
984
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
952
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
0
replies
932
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
1
reply
878
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
rmash
▴ 20
2
votes
3
replies
844
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
2
votes
2
replies
829
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
0
votes
0
replies
486
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
9 months ago
amir
• 0
24 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
marka
• 0
As a single dad in Australia, finding time to unwind is rare, but [Lincoln Casino][1] has become my go-to escape after putting the kids to …
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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Gordon Smyth
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Michael Love
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