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Covariates
•
reset
4
votes
4
replies
1.2k
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
6 months ago • updated 5 months ago
sukeshinik5
▴ 20
0
votes
0
replies
737
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
17 months ago
amir
• 0
5
votes
10
replies
2.7k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR
differential expression analysis
covariates
updated 4.5 years ago by
Gordon Smyth
52k • written 4.5 years ago by
Lucy
▴ 60
2
votes
3
replies
1.0k
views
Drug response pre- and post-treatment between timepoints across conditions
RNA-seq
Paired design
Timecourse
Diagnosis
Covariates
updated 4.8 years ago by
Kevin Blighe
★ 4.0k • written 4.8 years ago by
ibrahim.akkouh
• 0
0
votes
1
reply
1.1k
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2
rna-sequencing
covariates
glm
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
rmash
▴ 20
0
votes
3
replies
1.2k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
dhwani2410
• 0
3
votes
4
replies
1.2k
views
How to check whether experimental covariates are confounded with our group of interest?
covariates
microarray
5.2 years ago
english.server
▴ 20
2
votes
2
replies
977
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
Manik Garg
▴ 20
5
votes
9
replies
2.0k
views
limma Multi-level Experiments correcting for continuous covariates
limma
epic
methylation
limma design matrix
covariates
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
c.bettencourt
• 0
0
votes
2
replies
1.9k
views
Removing batch effect from gene expression before Limma linear modelling
Limma
differential gene expression
batch effect correction
covariates
updated 6.5 years ago by
Gordon Smyth
52k • written 6.5 years ago by
abelsousa
• 0
3
votes
4
replies
1.4k
views
Agilent Single-Channel Data: Questions about model statement and model building.
limma
agilent
microarray
covariates
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
CantExitVIM
▴ 10
2
votes
4
replies
5.7k
views
Age covariate continuous vs. categorical
deseq2
linear model
covariates
age
design model
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
L_K
• 0
0
votes
0
replies
1.1k
views
How to specify covariates in maSigPro analysis (like limma)
masigpro
covariates
limma
differential expression
time-course
7.2 years ago
veersingh.marwah
• 0
1
vote
4
replies
22k
views
Adjusting for covariates in paired sample design DESeq2
deseq2
deseq
paired samples
covariates
multiple time points
7.2 years ago
imb
▴ 10
0
votes
1
reply
1.8k
views
DESeq2 biological replicates and RIN values
deseq2
differential gene expression
covariates
rnaseq
updated 7.2 years ago by
Michael Love
43k • written 7.3 years ago by
pmoranlosada
• 0
2
votes
3
replies
11k
views
DESeq2 model with covariates
deseq2
covariates
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
markus.schulze
• 0
3
votes
19
replies
4.1k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.7 years ago
mheydarpour
▴ 10
0
votes
4
replies
2.9k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
8.1 years ago
j.viana
• 0
5
votes
8
replies
9.7k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 8 months ago by
hortense96
• 0 • written 8.4 years ago by
dmcleanuk
▴ 30
2
votes
3
replies
1.7k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 8.6 years ago by
chris86
▴ 420 • written 8.7 years ago by
TP
• 0
3
votes
3
replies
3.5k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.7 years ago
AST
▴ 60
1
vote
2
replies
2.1k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.7 years ago by
Michael Love
43k • written 8.7 years ago by
Mattia
▴ 10
4
votes
3
replies
10k
views
How do I extract read counts from DESeq2
deseq2
counts
covariates
updated 8.8 years ago by
Michael Love
43k • written 8.8 years ago by
hechtp
▴ 10
0
votes
0
replies
1.9k
views
limma: blocking factors and factorial design
limma
differential gene expression
design and contrast matrix
covariates
8.9 years ago
jlerga
• 0
0
votes
2
replies
3.2k
views
LIMMA Adjustment for Covariates
limma
covariates
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
trinhpauline
• 0
25 results • Page
1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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