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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 6.0 years ago by
James W. MacDonald
68k • written 6.0 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: DiffBind; Error: No sites have activity greater than filter value
by
etiennedanis
• 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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