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designmatrix
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
11 months ago
Tadeoye
▴ 20
0
votes
1
reply
564
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Neha
• 0
0
votes
3
replies
977
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
prity6459
• 0
0
votes
1
reply
589
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Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
avery
• 0
3
votes
5
replies
1.7k
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Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
aditya.m
▴ 10
4
votes
6
replies
1.8k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
3.0 years ago
Abdul
▴ 20
2
votes
4
replies
2.1k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2
limma
modelmatrix
edgeR
designmatrix
updated 4.1 years ago by
Gordon Smyth
53k • written 4.1 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.6k
views
DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix
deseq2
DESeq2
updated 4.1 years ago by
swbarnes2
★ 1.4k • written 4.1 years ago by
OST
• 0
1
vote
2
replies
1.6k
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multifactorial design matrix
designmatrix
RNA-seq
limma
updated 4.7 years ago by
Gordon Smyth
53k • written 4.7 years ago by
athief
▴ 20
1
vote
0
replies
991
views
Design Matrix for multiple variables in Edge R
designmatrix
DifferentialExpression
edgeR
RNAseq
4.8 years ago
nageshprabhu.k
▴ 10
2
votes
4
replies
1.5k
views
edgeR design matrix for multiple factors
MutlipleFactors
DesignMatrix
edgeR
4.8 years ago
Debayan
▴ 20
0
votes
2
replies
1.5k
views
Help creating a paired sample design matrix in edgeR
edgeR
pairedsamples
designmatrix
4.8 years ago
sfidemw
• 0
0
votes
2
replies
1.2k
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
anshulmbi
• 0
0
votes
2
replies
1.3k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger
r
differentialanalysis
rnaseq
designmatrix
updated 6.6 years ago by
Aaron Lun
★ 29k • written 6.6 years ago by
Beginner
▴ 60
2
votes
6
replies
1.7k
views
Limma DesignMatrix, dropping terms
Limma
designMatrix
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
Keifa
▴ 10
2
votes
4
replies
1.9k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 9.3 years ago by
Aaron Lun
★ 29k • written 9.3 years ago by
nashchem
• 0
16 results • Page
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Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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