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log2
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3
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6
replies
1.8k
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2
edgeR
RNA
limma
Normalization
16 months ago
Sara
• 0
6
votes
8
replies
5.6k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 16 months ago by
James W. MacDonald
65k • written 8.0 years ago by
serpalma.v
▴ 60
3
votes
1
reply
1.3k
views
log2 of normalized counts for further analyzes
DESeq2
log2
normalized
counts
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Laia
▴ 10
0
votes
1
reply
860
views
First time Statistical Analysis of RNA-seq
edgeR
RNA-Seq
log2
foldchange
q_value
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
johndavidgriner74
• 0
0
votes
8
replies
2.5k
views
DESeq2 different log2FC and p-value filtering parameters results comparison
log2
DESeq2
20 months ago
User000
• 0
2
votes
4
replies
3.0k
views
exporting limma log2 data
limma
export
log2
data
agilent
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
Jahn Davik
▴ 110
0
votes
1
reply
1.9k
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
Lara
• 0
0
votes
0
replies
910
views
PROBLEM WITH MFUZZ
mfuzz
fold change
log2
STANDARDISATION
5.8 years ago
prakashpandey1111
• 0
0
votes
0
replies
1.3k
views
DESeq2: Extract mean normalized log2 counts by level
normalized counts
log2
5.5 years ago
agdif
▴ 10
0
votes
0
replies
769
views
NMF pre-processsing effect on classification
NMF
log2
classification
bioconductor
5.8 years ago
Seymoo
• 0
10 results • Page
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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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