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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
5 months ago
Tadeoye
▴ 20
0
votes
1
reply
453
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Neha
• 0
0
votes
3
replies
794
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 13 months ago by
Gordon Smyth
52k • written 13 months ago by
prity6459
• 0
0
votes
1
reply
474
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 13 months ago by
Gordon Smyth
52k • written 13 months ago by
avery
• 0
3
votes
5
replies
1.5k
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
aditya.m
▴ 10
4
votes
6
replies
1.6k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
2.4 years ago
Abdul
▴ 20
2
votes
4
replies
1.8k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2
limma
modelmatrix
edgeR
designmatrix
updated 3.6 years ago by
Gordon Smyth
52k • written 3.6 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.5k
views
DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix
deseq2
DESeq2
updated 3.6 years ago by
swbarnes2
★ 1.4k • written 3.6 years ago by
OST
• 0
1
vote
2
replies
1.4k
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 4.1 years ago by
Gordon Smyth
52k • written 4.2 years ago by
athief
▴ 20
1
vote
0
replies
899
views
Design Matrix for multiple variables in Edge R
designmatrix
DifferentialExpression
edgeR
RNAseq
4.3 years ago • updated 4.2 years ago
nageshprabhu.k
▴ 10
2
votes
4
replies
1.3k
views
edgeR design matrix for multiple factors
MutlipleFactors
DesignMatrix
edgeR
4.3 years ago
Debayan
▴ 20
0
votes
2
replies
1.3k
views
Help creating a paired sample design matrix in edgeR
edgeR
pairedsamples
designmatrix
4.3 years ago
sfidemw
• 0
0
votes
2
replies
1.0k
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 5.1 years ago by
Michael Love
43k • written 5.1 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 6.0 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Beginner
▴ 60
2
votes
6
replies
1.5k
views
Limma DesignMatrix, dropping terms
Limma
designMatrix
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
Keifa
▴ 10
2
votes
4
replies
1.6k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
nashchem
• 0
16 results • Page
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Answer: Limma suqeezeVar
by
Gordon Smyth
52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
Comment: Discrepancies in normalised count data vs unnormalised
by
swbarnes2
★ 1.4k
Well, that's going to make each sample normalize quite differently. So you should expect large difference between normalized and unnormali…
Comment: Can't install BioC packages (and manager) behind firewall
by
Marcel Ramos
700
Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…
Comment: Limma trend with limpa
by
Alejandro
• 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error
by
asafpr
• 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Votes
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
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