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Showing :
Voom
•
reset
1
vote
6
replies
2.7k
views
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
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
7
votes
2
replies
880
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
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
2
votes
4
replies
649
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
6 months ago
Tyler Sagendorf
▴ 10
5
votes
2
replies
612
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
3
votes
4
replies
571
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
6 months ago
pl23
• 0
0
votes
1
reply
481
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
1
vote
2
replies
297
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
14 days ago • updated 13 days ago
Dylan.Sheerin
• 0
0
votes
2
replies
210
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
7 weeks ago
Gimena
• 0
0
votes
2
replies
197
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 4 weeks ago by
taur.vil
• 0
12 results • Page
1 of 1
Recent ...
Replies
Answer: Get gene symbols for a set of hg19 coordinates
by
ATpoint
★ 4.1k
Simply download a GTF file (for example from GENCODE) matching the current genome and/or annotation version you are using in your project a…
Comment: Not able to install any Bioconductor 3.18 package [unable to access index]
by
ATpoint
★ 4.1k
Try the mirror suggestion for now: https://support.bioconductor.org/p/9153734/#9153755
Comment: unable to access bioconductor packages - qvalue installation failed...
by
ATpoint
★ 4.1k
Seems to be a general problem at the moment, can reproduce. The the mirror suggestion here: https://support.bioconductor.org/p/9153734/#915…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
Karosham.Reddy
• 0
Thank you for the suggestion the ENmix version is using is ENmix_1.38.01. I tried your suggested code, R identified the idat files but sti…
Comment: pathview error
by
Guido Hooiveld
★ 4.0k
> Will removing the NA values help solve the problem? Did you try? And, FWIW, in the cases I had ensembl-based RNA-seq datasets I removed…
Votes
Comment: recount3 problem downloading data from source sra
Not able to install any Bioconductor 3.18 package [unable to access index]
unable to access bioconductor packages - qvalue installation failed...
Not able to install any Bioconductor 3.18 package [unable to access index]
can't open mghp.osn.xsede.org
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