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time series
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1
vote
8
replies
1.8k
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time series, block by patient, between and within comparisons limma-voom
rna-seq
time series
patient
limma-voom
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
aec
▴ 90
4
votes
7
replies
3.2k
views
LIMMA time series spline model.matrix design setup
limma
design
model.matrix
time series
splines
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
tleona3
• 0
0
votes
4
replies
1.3k
views
DESeq2 multifactor formula design
deseq2
time series
multiple factor design
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
Jane
• 0
1
vote
2
replies
1.3k
views
DESeq2: RNA-Seq time series analysis after removal of batch effect
deseq2
time series
remove batch effect
5.2 years ago
Nicola
• 0
1
vote
2
replies
2.0k
views
DeSEQ2- What is the difference between Gene Clustering and using LRT for Time Series experiment WITHOUT treatments
deseq2
Time Series
Gene Clustering
LRT
ATACseq
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
kaiser.karim
• 0
1
vote
2
replies
1.5k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma
microarray
time series
DEG
paired
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
kawess
• 0
1
vote
2
replies
841
views
Time series experiment analysis in DEseq2 without T=0 and three independent experiments with linked samples
deseq2
rnaseq
repeated measures
time series
design formula
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
Dorien
▴ 10
3
votes
2
replies
2.2k
views
DESeq2 time course model
deseq2
time series
time course
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
bsierieb
▴ 10
7
votes
2
replies
3.2k
views
Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2
ruvseq
spike-in
time course
time series
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
staceyborrego
▴ 20
0
votes
2
replies
1.0k
views
Design matrix choice for time series experiment using limma
limma
time series
help
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
rm1238
• 0
0
votes
0
replies
662
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq
time series
3.8 years ago
Bogdan
▴ 670
1
vote
0
replies
866
views
Job:
Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics
gene expression
time series
plant biology
circadian
Job
4.6 years ago
dezer
▴ 10
12 results • Page
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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