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limmagui
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limma model matrix questions
limmaGUI
limma
pairedsamples
5 weeks ago
whyw6948
• 0
0
votes
1
reply
166
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Main effect on multiple comparisons in limma
limmaGUI
lim
MultipleComparison
multip
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
roger.moreno.justicia
• 0
1
vote
4
replies
287
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jitendra
▴ 10
1
vote
5
replies
943
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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 8 months ago by
Gordon Smyth
50k • written 9 months ago by
manuelsokolov
• 0
0
votes
1
reply
585
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
qiz218591
• 0
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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