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designmatrix
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0
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307
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
6 weeks ago
Tadeoye
▴ 20
0
votes
1
reply
357
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 7 months ago by
James W. MacDonald
67k • written 7 months ago by
Neha
• 0
0
votes
3
replies
635
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
396
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 3.3 years ago by
swbarnes2
★ 1.4k • written 3.3 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
842
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
4.0 years ago • updated 3.9 years ago
sfidemw
• 0
0
votes
2
replies
931
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
1.1k
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
16 results • Page
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Replies
Comment: How can I generate a heatmap and clustering of differentially expressed genes in
by
Renuka
• 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Comment: Is there a way to do DEG analysis across two batches sharing one sample only?
by
georgeyu703
• 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only?
by
Michael Love
43k
Yes, with the knowledge that, it is expected to be underpowered.
Comment: Is there a way to do DEG analysis across two batches sharing one sample only?
by
georgeyu703
• 0
Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?
Answer: Is there a way to do DEG analysis across two batches sharing one sample only?
by
Michael Love
43k
The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confoundeā¦
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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