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roast
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6
votes
10
replies
1.8k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing
roast
mroast
differential gene expression
bioconductor
8.9 years ago
svlachavas
▴ 830
4
votes
6
replies
3.8k
views
limma roast syntax and interpretation
limma
roast
updated 9.5 years ago by
Gordon Smyth
50k • written 9.5 years ago by
Juliet Hannah
▴ 360
1
vote
4
replies
1.2k
views
Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
limma
roast
statistics
source code
gene set testing
5.7 years ago
Andrea Carenzo
• 0
4
votes
4
replies
1.4k
views
Interpreting mroast results
mroast
limma
roast
5.4 years ago
SB
• 0
3
votes
4
replies
2.4k
views
edgeR: no replicates & mroast
edger
roast
updated 9.4 years ago by
Gordon Smyth
50k • written 9.4 years ago by
Daniel
▴ 10
0
votes
3
replies
1.4k
views
ROAST using curated gene sets
edgeR
mroast
roast
7.9 years ago
lattalic
• 0
3
votes
2
replies
1.2k
views
Self-contained gene set testing with DESeq2 results
roast
DESeq2
GeneSetEnrichment
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
prabin.dm
• 0
2
votes
2
replies
1.2k
views
Running Roast with Gene Symbols of Curated Genes
mroast
roast
gene set
gene set analysis
edgeR
updated 7.9 years ago by
James W. MacDonald
65k • written 7.9 years ago by
lattalic
• 0
2
votes
2
replies
1.3k
views
limma roast/mroast with patient-matched pre-/post- treatment
limma
roast
mroast
block
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
barbara.shih
• 0
3
votes
2
replies
1.2k
views
ROAST after edgeR glmTreat and average RPKM filter
roast
edgeR
glmtreat
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
b.nota
▴ 360
2
votes
2
replies
1.5k
views
limma roast results not in accordance with barcodeplot
roast
limma
6.0 years ago
b.nota
▴ 360
2
votes
2
replies
1.6k
views
Finding genes in a gene set detected by ROAST (or FRY) in limma
roast
fry
limma
updated 4.8 years ago by
Gordon Smyth
50k • written 4.8 years ago by
kentfung
▴ 20
2
votes
1
reply
1.3k
views
limma symbols2indices from gmt files versus rdata files
limma
romer
roast
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
biominer
▴ 10
13 results • Page
1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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