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logfc
•
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0
votes
0
replies
658
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
18 months ago
Tadeoye
▴ 20
5
votes
6
replies
2.2k
views
LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
2.5 years ago
JK Kim
▴ 20
2
votes
4
replies
1.5k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
3.2 years ago
mbenegas
▴ 10
2
votes
4
replies
2.6k
views
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma
toptable
deg
logfc
written 6.2 years ago by
Biomed
• 0
3
votes
4
replies
3.4k
views
Calculation of logFC in edgeR
edgeR
logfc
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
H
▴ 20
4
votes
2
replies
1.7k
views
Limma: how to interpret logFC for interaction contrast
limma
logFC
factor interaction
updated 4.4 years ago by
James W. MacDonald
67k • written 4.4 years ago by
Natalia
• 0
7
votes
6
replies
24k
views
Conversion of LogFC to FC
limma
logfc
fc
updated 4.7 years ago by
Gordon Smyth
51k • written 4.7 years ago by
nia
▴ 30
3
votes
1
reply
831
views
logFC in limma
limma
logFC
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
gv
▴ 40
0
votes
0
replies
948
views
DEP package - Understanding the results table
dep
proteomics
logFC
5.1 years ago
rina
▴ 30
1
vote
5
replies
2.9k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 5.7 years ago by
Gordon Smyth
51k • written 5.7 years ago by
xingxd16
▴ 20
1
vote
3
replies
3.7k
views
the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?
edger
limma
logfc
updated 21 months ago by
Gordon Smyth
51k • written 6.1 years ago by
ZihaoXing
• 0
1
vote
4
replies
1.6k
views
Methylation EPIC annotation - the logFC values represented as boxplots
probe to gene id
logFC
illuminahumanmethylationepicanno.ilm10b2.hg19
limma contrast matrix
updated 6.6 years ago by
James W. MacDonald
67k • written 6.6 years ago by
jonellevillar
• 0
17
votes
14
replies
45k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 2.4 years ago by
OE
• 0 • written 7.3 years ago by
cms72
▴ 20
5
votes
5
replies
3.2k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR
logFC
FPKM
updated 8.1 years ago by
Gordon Smyth
51k • written 8.1 years ago by
Sara
▴ 20
0
votes
6
replies
2.8k
views
paired analysis using metagenomeSeq
metagenomeseq
logfc
paired samples
standard error
updated 2.3 years ago by
tom830979
• 0 • written 8.1 years ago by
manasishah86
▴ 30
0
votes
1
reply
1.6k
views
Question on fold change calculation for microarray data
logfc
limma
fold change
updated 8.2 years ago by
Gordon Smyth
51k • written 8.2 years ago by
Claudia
▴ 10
1
vote
5
replies
14k
views
Limma LogFC hand calculation
limma
logfc
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
cookm346
• 0
4
votes
9
replies
2.6k
views
LIMMA gives different logFC
limma
LogFC
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
beginner
• 0
9
votes
7
replies
2.0k
views
EdgeR returns small logFC values when using GLM approach
edger
glm
logfc
8.6 years ago
gergely.zsuzsa.n
• 0
7
votes
2
replies
6.2k
views
What is logFC and "B" in methylation analysis ??
limma
champ
logfc
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
AST
▴ 60
1
vote
6
replies
6.7k
views
fold change calculation in edger
edger
normalization
logfc
updated 8.8 years ago by
Michael Love
42k • written 8.8 years ago by
tonja.r
▴ 80
4
votes
4
replies
3.7k
views
Determining direction of logFC in limma
logFC
limma
9.0 years ago
pt2395
• 0
1
vote
1
reply
1.9k
views
Data handling in DESeq2
deseq2
data handling
comparing more than two groups
normalization
logfc
updated 9.0 years ago by
Michael Love
42k • written 9.0 years ago by
bioboy
• 0
1
vote
3
replies
1.9k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 9.2 years ago by
Aaron Lun
★ 28k • written 9.2 years ago by
amoltej
▴ 10
2
votes
2
replies
2.6k
views
limma: Using log2 fold changes as input for a linear model fit
limma
logfc
lmfit
updated 9.4 years ago by
Aaron Lun
★ 28k • written 9.4 years ago by
Moritz E. Beber
▴ 10
1
vote
8
replies
3.9k
views
Intepretation of RUVseq/edgeR logFC
RUVseq
logFC
edgeR
9.5 years ago
Marie
• 0
5
votes
4
replies
22k
views
Report and compare log2FC vs FC
deseq2
logfc
updated 9.6 years ago by
smoorthie
▴ 10 • written 9.6 years ago by
Catalina Aguilar Hurtado
▴ 90
2
votes
1
reply
3.9k
views
Difference between DESeq2 versions and explanation of betaPrior = False and padj
DESeq2
LogFC
Adjusted pvalue
updated 9.8 years ago by
Michael Love
42k • written 9.8 years ago by
madal
• 0
0
votes
3
replies
3.8k
views
[limma - v. 17 June 2014] Log2 or not to log2 the data? (Agilent single-channel microarray data)
limma
logFC
normalizeBetweenArrays()
10.0 years ago
FAVI
• 0
29 results • Page
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Comment: How many of my genes from my gene list are in each KEGG pathway?
by
josephasmith1310
• 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open!
by
Esperan
• 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
by
Gordon Smyth
51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples
by
txema.heredia
• 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells
by
Michael Love
42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Votes
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
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