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adjustment
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4
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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
10 months ago
sukeshinik5
▴ 20
1
vote
1
reply
1.1k
views
DEP p.val adjustment
DEP
P.vals
adjustment
updated 6.1 years ago by
James W. MacDonald
68k • written 6.1 years ago by
826599
▴ 10
1
vote
2
replies
2.6k
views
How to adjust for different cell type mixtures in differential expression analysis?
cell types
differential expression
adjustment
mixtures
rnaseq
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
aec
▴ 90
0
votes
4
replies
5.4k
views
RNAseq Adjusting for Covariates?
RNA
rnaseq
Covariate
adjustment
deseq
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
sjs0282
• 0
1
vote
9
replies
4.2k
views
LIMMA for paired analysis with adjustment for confounding continuous variables
limma
gene expression
confounding
adjustment
paired
9.5 years ago
Loodramon
• 0
13
votes
2
replies
7.2k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma
covariate
continuous
categorical
adjustment
updated 9.8 years ago by
Gordon Smyth
52k • written 9.8 years ago by
sg45653
• 0
6 results • Page
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Comment: Cannot extract size factor from DESeq2 analysis
by
s.malik
• 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function
by
Vishnu
• 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2
by
Tom
• 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function
by
ATpoint
★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq
by
caroline.zanchi
• 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
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