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Showing :
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
sukeshinik5
▴ 20
0
votes
0
replies
744
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
18 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
1.1k
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 5.2 years ago by
Martin Morgan
25k • written 5.2 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
5.3 years ago
english.server
▴ 20
2
votes
2
replies
978
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 5.6 years ago by
Michael Love
43k • written 5.6 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 6.6 years ago by
Gordon Smyth
52k • written 6.6 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 6.7 years ago by
Gordon Smyth
52k • written 6.7 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
23k
views
Adjusting for covariates in paired sample design DESeq2
deseq2
deseq
paired samples
covariates
multiple time points
7.3 years ago
imb
▴ 10
0
votes
1
reply
1.8k
views
DESeq2 biological replicates and RIN values
deseq2
differential gene expression
covariates
rnaseq
updated 7.3 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
4.2k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.8 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 8.7 years ago by
chris86
▴ 420 • written 8.7 years ago by
TP
• 0
3
votes
3
replies
3.6k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.8 years ago • updated 8.7 years ago
AST
▴ 60
1
vote
2
replies
2.1k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.8 years ago by
Michael Love
43k • written 8.8 years ago by
Mattia
▴ 10
4
votes
3
replies
11k
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
9.0 years ago
jlerga
• 0
0
votes
2
replies
3.2k
views
LIMMA Adjustment for Covariates
limma
covariates
updated 9.0 years ago by
Aaron Lun
★ 28k • written 9.0 years ago by
trinhpauline
• 0
25 results • Page
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
by
ATpoint
★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format
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ControlF5
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Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
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EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
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• 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts
by
O'Brien
• 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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