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mroast
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611
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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
4
votes
4
replies
1.4k
views
Interpreting mroast results
mroast
limma
roast
5.4 years ago
SB
• 0
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
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
0
votes
2
replies
903
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
3
votes
3
replies
903
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
818
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
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
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
2
replies
1.5k
views
using camera/roast/romer to find enriched gene sets from proteomics data
limma
proteomics
camera
mroast
romer
updated 7.5 years ago by
Gordon Smyth
50k • written 7.5 years ago by
natalia.pietrosemoli
• 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
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
3
replies
1.4k
views
ROAST using curated gene sets
edgeR
mroast
roast
7.9 years ago
lattalic
• 0
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
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
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
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
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
0
votes
1
reply
1.5k
views
Graphic representation of mroast results
mroast
visualization
8.9 years ago
Elena Serrano
▴ 30
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
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
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
22 results • Page
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Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
gabriel.hoffman
▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded
by
W. Evan Johnson
▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis
by
Alejandro Reyes
★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object
by
Alejandro Reyes
★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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