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gene set testing
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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
3.7 years ago
svlachavas
▴ 830
4
votes
11
replies
2.1k
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 4.5 years ago by
Robert Castelo
★ 3.3k • written 4.5 years ago by
Jeremy Beales
▴ 10
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 5.7 years ago by
Gordon Smyth
51k • written 5.7 years ago by
svlachavas
▴ 830
7
votes
2
replies
1.4k
views
Pre-ranked camera gene set testing with edgeR results
limma
camera
cameraPR
edgeR
gene set testing
updated 5.8 years ago by
Gordon Smyth
51k • written 5.8 years ago by
jamie.gearing
▴ 60
1
vote
4
replies
1.3k
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
5.8 years ago
Andrea Carenzo
• 0
0
votes
1
reply
1.3k
views
GAGE function and the same.dir option
gage
gene set testing
updated 6.1 years ago by
Luo Weijun
★ 1.6k • written 6.1 years ago by
Aurora
▴ 20
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 5 weeks ago by
Chris
▴ 10 • written 7.5 years ago by
Pekka Kohonen
▴ 190
4
votes
6
replies
2.0k
views
Gene set Testing with Limma for Agilent IDs probes?
limma
agilent microarrays
gene set testing
annotation
7.4 years ago
Bouzid.a
▴ 20
7
votes
13
replies
2.3k
views
Test whether expression levels of two gene sets are significantly different
R
DESeq2
gene set testing
gene expression
7.6 years ago
Jon Bråte
▴ 250
3
votes
4
replies
1.6k
views
Competitive gene set testing between two sets of genes
gene set testing
camera
edger
updated 7.9 years ago by
Gordon Smyth
51k • written 8.0 years ago by
le2336
▴ 20
1
vote
0
replies
1.4k
views
Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
gsea
ncrna
coexpression
gene set analysis
gene set testing
8.1 years ago
m.fletcher
▴ 20
1
vote
5
replies
2.1k
views
Confused by results from CAMERA gene set testing
limma
camera
gene set testing
8.2 years ago
claire.n.levy
▴ 10
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 8.5 years ago by
Gordon Smyth
51k • written 8.5 years ago by
svlachavas
▴ 830
6
votes
10
replies
1.9k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing
roast
mroast
differential gene expression
bioconductor
9.1 years ago
svlachavas
▴ 830
14 results • Page
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Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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