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designmatrix
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0
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2
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256
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
12 days ago • updated 11 days ago
Tadeoye
▴ 20
0
votes
1
reply
338
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
588
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
380
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 3.2 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
827
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
915
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
16 results • Page
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Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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