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Fold Change
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5
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14
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4.7k
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Possible ways to select differential expressed genes using DeSeq2 or edgeR
R
deseq2
edger
differential gene expression
fold change
updated 22 months ago by
ATpoint
★ 3.9k • written 5.7 years ago by
Beginner
▴ 60
1
vote
2
replies
2.1k
views
diffBind report Fold scale
diffBind
Fold Change
updated 2.9 years ago by
Joe Nicholas
• 0 • written 5.2 years ago by
joseluis.ruiz
• 0
2
votes
4
replies
1.2k
views
Majority upregulated genes in edgeR
edger
differential expression
genes
fold change
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
ilovesuperheroes1993
• 0
0
votes
0
replies
901
views
PROBLEM WITH MFUZZ
mfuzz
fold change
log2
STANDARDISATION
5.7 years ago
prakashpandey1111
• 0
1
vote
1
reply
1.3k
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 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
ag1805x
▴ 80
0
votes
1
reply
1.5k
views
Question on fold change calculation for microarray data
logfc
limma
fold change
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
Claudia
▴ 10
2
votes
7
replies
2.3k
views
About differentially expressed genes that found by edgeR
edgeR
DE analysis
fold change
cpm
updated 7.6 years ago by
Ryan C. Thompson
★ 7.9k • written 7.6 years ago by
Sara
▴ 10
7 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
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