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Designmatrix
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
20 days ago • updated 19 days ago
Tadeoye
▴ 20
0
votes
1
reply
344
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
609
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
384
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
2.1 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 3.2 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 3.8 years ago by
athief
▴ 20
1
vote
0
replies
831
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
921
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 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
nashchem
• 0
16 results • Page
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
by
ATpoint
★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format
by
ControlF5
• 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open!
by
Alan Downey
• 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
by
O'Brien
• 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts
by
O'Brien
• 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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