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DesignMatrix
•
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0
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2
replies
715
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
12 months ago
Tadeoye
▴ 20
0
votes
1
reply
571
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
982
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
594
views
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
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 2.9 years ago by
Michael Love
43k • written 2.9 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 4.2 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.7k
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
views
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
997
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 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
nashchem
• 0
16 results • Page
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Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
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