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designMatrix
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0
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2
replies
297
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
5 weeks ago
Tadeoye
▴ 20
0
votes
1
reply
353
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 6 months ago by
James W. MacDonald
67k • written 6 months ago by
Neha
• 0
0
votes
3
replies
634
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
prity6459
• 0
0
votes
1
reply
392
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
avery
• 0
3
votes
5
replies
1.3k
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 24 months ago by
Michael Love
43k • written 24 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
2.1 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 3.2 years ago by
Gordon Smyth
52k • written 3.3 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 3.8 years ago by
Gordon Smyth
52k • written 3.8 years ago by
athief
▴ 20
1
vote
0
replies
839
views
Design Matrix for multiple variables in Edge R
designmatrix
DifferentialExpression
edgeR
RNAseq
3.9 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
929
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.8 years ago by
Michael Love
43k • written 4.8 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 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Beginner
▴ 60
2
votes
6
replies
1.4k
views
Limma DesignMatrix, dropping terms
Limma
designMatrix
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
Keifa
▴ 10
2
votes
4
replies
1.5k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
nashchem
• 0
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Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
Jonathan
▴ 10
Thank you; I was indeed using `DGEList` on the count matrix, but with the multiple edits of the post I forgot to include this step. BTW, …
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
67k
The other reason for doing this is because when you do `topTable(fit)`, you will automatically annotate the output data.
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
67k
If you have versioned Ensembl Gene IDs, you can always use "GENEIDVERSION" for the `select` statement, or just strip off the version number…
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
67k
You say you have a matrix of counts, but that's not what you should be using. Instead you should be using a `DGEList` object. I would norma…
Comment: Problems with oarfish + tximport + swish
by
brown.annaleigh
• 0
More failures encountered k_skip = tximeta(coldata = data.frame(files = m, names = names(m)), type = 'oarfish',…
Votes
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
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