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DesignMatrix
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0
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2
replies
243
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
8 days ago
Tadeoye
▴ 20
0
votes
1
reply
335
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 5 months ago by
James W. MacDonald
67k • written 5 months ago by
Neha
• 0
0
votes
3
replies
583
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 8 months ago by
Gordon Smyth
52k • written 8 months ago by
prity6459
• 0
0
votes
1
reply
377
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 8 months ago by
Gordon Smyth
52k • written 8 months ago by
avery
• 0
3
votes
5
replies
1.3k
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 23 months ago by
Michael Love
43k • written 23 months ago by
aditya.m
▴ 10
4
votes
6
replies
1.5k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
2.0 years ago
Abdul
▴ 20
2
votes
4
replies
1.7k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2
limma
modelmatrix
edgeR
designmatrix
updated 3.1 years ago by
Gordon Smyth
52k • written 3.2 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.4k
views
DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix
deseq2
DESeq2
updated 3.2 years ago by
swbarnes2
★ 1.4k • written 3.2 years ago by
OST
• 0
1
vote
2
replies
1.3k
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
athief
▴ 20
1
vote
0
replies
825
views
Design Matrix for multiple variables in Edge R
designmatrix
DifferentialExpression
edgeR
RNAseq
3.8 years ago
nageshprabhu.k
▴ 10
2
votes
4
replies
1.2k
views
edgeR design matrix for multiple factors
MutlipleFactors
DesignMatrix
edgeR
3.9 years ago
Debayan
▴ 20
0
votes
2
replies
1.2k
views
Help creating a paired sample design matrix in edgeR
edgeR
pairedsamples
designmatrix
3.9 years ago
sfidemw
• 0
0
votes
2
replies
914
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
anshulmbi
• 0
0
votes
2
replies
1.0k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger
r
differentialanalysis
rnaseq
designmatrix
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
Beginner
▴ 60
2
votes
6
replies
1.4k
views
Limma DesignMatrix, dropping terms
Limma
designMatrix
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
Keifa
▴ 10
2
votes
4
replies
1.5k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
nashchem
• 0
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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
James W. MacDonald
67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
anna.cot.anna.cot
▴ 30
Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
James W. MacDonald
67k
Please come back to the support site and view your post - I've fixed it for you. If you want to show people your targets file, just paste t…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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