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fold change
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Possible ways to select differential expressed genes using DeSeq2 or edgeR
R
deseq2
edger
differential gene expression
fold change
updated 17 months ago by
ATpoint
★ 3.4k • written 5.2 years ago by
Beginner
▴ 50
1
vote
2
replies
1.8k
views
diffBind report Fold scale
diffBind
Fold Change
updated 2.4 years ago by
Joe Nicholas
• 0 • written 4.7 years ago by
joseluis.ruiz
• 0
2
votes
4
replies
922
views
Majority upregulated genes in edgeR
edger
differential expression
genes
fold change
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
ilovesuperheroes1993
• 0
0
votes
0
replies
709
views
PROBLEM WITH MFUZZ
mfuzz
fold change
log2
STANDARDISATION
5.2 years ago
prakashpandey1111
• 0
1
vote
1
reply
1.1k
views
What is the exact formula for the calculation of Fold Change (FC), p-val and q-val in Ballgown stattest?
ballgown
stattest
fold change
updated 5.5 years ago by
James W. MacDonald
63k • written 5.5 years ago by
ag1805x
▴ 80
0
votes
1
reply
1.4k
views
Question on fold change calculation for microarray data
logfc
limma
fold change
updated 7.1 years ago by
Gordon Smyth
48k • written 7.1 years ago by
Claudia
▴ 10
2
votes
7
replies
2.1k
views
About differentially expressed genes that found by edgeR
edgeR
DE analysis
fold change
cpm
updated 7.1 years ago by
Ryan C. Thompson
7.8k • written 7.1 years ago by
Sara
▴ 10
7 results • Page
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Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
James W. MacDonald
63k
No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
• 0
Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …
Votes
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Remove duplicates of colData in TreeSummarizedExperiment
Answer: Remove duplicates of colData in TreeSummarizedExperiment
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