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complex-design
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3
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4
replies
1.1k
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Complicated unbalanced block DOE with partially paired samples and analysis
limma
complex-design
paired design
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
ML18
▴ 10
0
votes
5
replies
2.2k
views
getting sample size for RNAseq experiment
rnaseqpower
sspa
sample size
sequencing
complex-design
updated 8.2 years ago by
m.van_iterson
▴ 20 • written 8.2 years ago by
roser.navarro
• 0
9
votes
21
replies
5.3k
views
limma - complex design with paired samples, sex and batch effect
limma
paired samples
complex-design
8.4 years ago • updated 8.3 years ago
aec
▴ 90
7
votes
6
replies
3.9k
views
Design and contrast question limma (additive or nested or duplicateCorrelation())??
limma
model matrix
limma design matrix
complex-design
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Guido Hooiveld
★ 3.9k
1
vote
1
reply
2.9k
views
Factorial Design with DESeq2; contrast problem.
deseq2
multiple factor design
complex-design
updated 9.1 years ago by
Michael Love
41k • written 9.1 years ago by
sifujio
• 0
1
vote
3
replies
6.6k
views
Combat - error - system is computationally singular
combat
software error
rnaseq
complex-design
updated 9.5 years ago by
Peter Langfelder
★ 3.0k • written 9.5 years ago by
Stefano Mangiola
▴ 10
7
votes
11
replies
2.3k
views
Using edgeR on pre-post treatment control design
edgeR
complex-design
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
lwc628
▴ 20
7 results • Page
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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…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
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)
biomaRt error: database disk image is malformed
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