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8
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Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.0 years ago • updated 8.9 years ago
AurelieMLB
▴ 50
5
votes
6
replies
2.3k
views
Translating model formula from DESeq to DEXSeq
dexseq
linear model
formula
updated 8.5 years ago by
Alejandro Reyes
★ 1.9k • written 8.5 years ago by
Cornwell, Adam
▴ 110
3
votes
8
replies
1.9k
views
Differential drug dosage effect between two genotypes in limma
limma
dose-response
linear model
model
formula
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
biominer
▴ 10
3
votes
7
replies
1.8k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2
twins
design
formula
RNA-seq
6.5 years ago
Simone
• 0
0
votes
8
replies
1.9k
views
Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
taveluz
• 0
0
votes
10
replies
2.4k
views
DEseq2 design formula correcting for batch
deseq2
design
formula
batch effect
updated 4.2 years ago by
swbarnes2
★ 1.3k • written 4.2 years ago by
l.rijnberk
• 0
0
votes
1
reply
748
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2
design
formula
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
Bine
▴ 40
0
votes
1
reply
956
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
estafana.t98
• 0
0
votes
5
replies
1.6k
views
Limma: how to account for twin data (both MZ and DZ twins)?
limma
design
RNA-seq
formula
twins
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
Simone
• 0
0
votes
5
replies
1.3k
views
DESeq2 design formula - correlation with ordered variable
DESeq2
design
formula
matrix
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
t.kuilman
▴ 170
0
votes
6
replies
1.3k
views
variancePartition - testing for individuals
variance
formula
expression
updated 5.3 years ago by
mikhael.manurung
▴ 270 • written 5.3 years ago by
rina
▴ 30
11 results • Page
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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