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mroast
•
reset
2
votes
6
replies
1.6k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast
limma
pathway analysis
differential gene expression
affymetrix
9.1 years ago
svlachavas
▴ 830
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
8
votes
4
replies
5.5k
views
Differences between edgeR's and limma+voom's implementation of camera/roast/romer
limma
edger
mroast
romer
camera
updated 8.2 years ago by
Steve Lianoglou
★ 13k • written 8.2 years ago by
maltethodberg
▴ 170
0
votes
4
replies
1.5k
views
Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast
limma
pathview
pathway analysis
updated 9.1 years ago by
Luo Weijun
★ 1.6k • written 9.1 years ago by
svlachavas
▴ 830
4
votes
4
replies
1.4k
views
Interpreting mroast results
mroast
limma
roast
5.4 years ago
SB
• 0
7
votes
9
replies
2.9k
views
limma's mroast and romer
romer
mroast
limma
updated 8.6 years ago by
Gordon Smyth
50k • written 8.6 years ago by
Ilario De Toma
▴ 10
0
votes
3
replies
1.4k
views
ROAST using curated gene sets
edgeR
mroast
roast
7.9 years ago
lattalic
• 0
0
votes
3
replies
1.9k
views
Barcodeplot limma function using two logFC lists
limma
edger
barcodeplot
gene set enrichment
mroast
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
srmaruyama
• 0
3
votes
3
replies
911
views
Conditions for using Fry
limma
mroast
fry
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
siajunren
• 0
3
votes
4
replies
819
views
Is number of rotations dependent on number of gene sets in mroast?
limma
mroast
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
siajunren
• 0
0
votes
2
replies
905
views
mroast/fry with gene weights for most or all genes
limma
mroast
fry
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
maltethodberg
▴ 170
2
votes
3
replies
1.4k
views
Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
limma
agilent microarrays
mroast
fry gene tests
gene set testing
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
svlachavas
▴ 830
1
vote
2
replies
1.3k
views
Explanation of mroast results for specific biological processes and error with barcodeplot function with a microarray dataset
limma
mroast
agilent microarrays
GO.BP
barcodeplot
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
svlachavas
▴ 830
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
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma
mroast
GSEA
GO
illumina human ht-12 v4
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
svlachavas
▴ 830
7
votes
10
replies
1.6k
views
Possible TF binding site enrichment analysis through mroast and conversion problems
TF binding site analysis
bioconductor
mroast
limma
promoter analysis
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
svlachavas
▴ 830
7
votes
6
replies
3.2k
views
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
limma
mroast
barcodeplot
KEGG
gene set testing
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
svlachavas
▴ 830
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
0
votes
2
replies
1.5k
views
using camera/roast/romer to find enriched gene sets from proteomics data
limma
proteomics
camera
mroast
romer
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
natalia.pietrosemoli
• 0
0
votes
6
replies
1.8k
views
Different results obtained from mroast and camera from Deseq2 counts
limma
camera
mroast
tximport
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
1.5k
views
Graphic representation of mroast results
mroast
visualization
8.9 years ago
Elena Serrano
▴ 30
0
votes
0
replies
614
views
Interpretation of mroast p-value results for gene set testing of specific molecular signatures using microarray data
mroast
camera
gene set testing
3.5 years ago
svlachavas
▴ 830
22 results • Page
1 of 1
Recent ...
Replies
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates
by
hortense96
• 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp
by
Basti
▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none
by
WardDeb
• 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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shepherl
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Gordon Smyth
50k
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taur.vil
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Yuan Tian
▴ 280
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Charlotte Soneson
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