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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
11 months ago
Tadeoye
▴ 20
0
votes
1
reply
562
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
975
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
586
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
avery
• 0
3
votes
5
replies
1.7k
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 2.8 years ago by
Michael Love
43k • written 2.8 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
2.0k
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 4.1 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.6k
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 4.6 years ago by
Gordon Smyth
53k • written 4.7 years ago by
athief
▴ 20
1
vote
0
replies
987
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 5.6 years ago by
Michael Love
43k • written 5.6 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
1.8k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 9.3 years ago by
Aaron Lun
★ 29k • written 9.3 years ago by
nashchem
• 0
16 results • Page
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList
by
Kevin Blighe
★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data
by
Kevin Blighe
★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot
by
Kevin Blighe
★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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