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gene set testing
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981
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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
5.2 years ago
svlachavas
▴ 840
4
votes
11
replies
3.6k
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 6.0 years ago by
Robert Castelo
★ 3.4k • written 6.0 years ago by
Jeremy Beales
▴ 10
2
votes
3
replies
1.9k
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 7.1 years ago by
Gordon Smyth
53k • written 7.1 years ago by
svlachavas
▴ 840
7
votes
2
replies
2.0k
views
Pre-ranked camera gene set testing with edgeR results
limma
camera
cameraPR
edgeR
gene set testing
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
jamie.gearing
▴ 60
1
vote
4
replies
1.8k
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
7.3 years ago
Andrea Carenzo
• 0
0
votes
1
reply
1.8k
views
GAGE function and the same.dir option
gage
gene set testing
updated 7.5 years ago by
Luo Weijun
★ 1.6k • written 7.5 years ago by
Aurora
▴ 20
2
votes
4
replies
2.4k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 19 months ago by
Chris
▴ 20 • written 8.9 years ago by
Pekka Kohonen
▴ 190
4
votes
6
replies
2.5k
views
Gene set Testing with Limma for Agilent IDs probes?
limma
agilent microarrays
gene set testing
annotation
8.9 years ago
Bouzid.a
▴ 20
7
votes
13
replies
3.3k
views
Test whether expression levels of two gene sets are significantly different
R
DESeq2
gene set testing
gene expression
9.1 years ago • updated 9.0 years ago
Jon BrĂ¥te
▴ 270
3
votes
4
replies
2.2k
views
Competitive gene set testing between two sets of genes
gene set testing
camera
edger
updated 9.4 years ago by
Gordon Smyth
53k • written 9.4 years ago by
le2336
▴ 20
1
vote
0
replies
1.8k
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
9.6 years ago
m.fletcher
▴ 20
1
vote
5
replies
2.7k
views
Confused by results from CAMERA gene set testing
limma
camera
gene set testing
9.6 years ago
claire.n.levy
▴ 10
7
votes
6
replies
3.8k
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 10.0 years ago by
Gordon Smyth
53k • written 10.0 years ago by
svlachavas
▴ 840
6
votes
10
replies
2.5k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing
roast
mroast
differential gene expression
bioconductor
10.5 years ago
svlachavas
▴ 840
14 results • Page
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Replies
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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