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complex-design
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3
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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
8.3 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 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 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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Answer: Error retrieving ensembl gene id using biomaRt...
by
James W. MacDonald
65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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