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Voom
•
reset
1
vote
6
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2.7k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 7.5 years ago by
Camila Orellana
▴ 10
1
vote
5
replies
1.1k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI
normalization
limma
voom
Normalization
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
3
votes
4
replies
567
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
6 months ago • updated 5 months ago
pl23
• 0
2
votes
4
replies
648
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
6 months ago
Tyler Sagendorf
▴ 10
5
votes
3
replies
724
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom
blocking
limma
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
193
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 29 days ago by
taur.vil
• 0
7
votes
2
replies
876
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
0
votes
2
replies
209
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
7 weeks ago • updated 6 weeks ago
Gimena
• 0
5
votes
2
replies
611
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
1
vote
2
replies
291
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
13 days ago • updated 12 days ago
Dylan.Sheerin
• 0
1
vote
1
reply
1.0k
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
0
votes
1
reply
480
views
How to do PFS after Voom + Limma DGE ?
RNASeqData
limma
voom
PFS
DGE
updated 11 months ago by
James W. MacDonald
66k • written 11 months ago by
manuelsokolov
• 0
12 results • Page
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Comment: Slightly different count plots from R and spreadsheet
by
ATpoint
★ 4.1k
I don't think it is the purpose of the support site to debug Excel behaviour. The issue might be how it combines replicates into a single v…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
Karosham.Reddy
• 0
Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?
Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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