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gene set testing
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635
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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
3.6 years ago
svlachavas
▴ 830
4
votes
11
replies
2.0k
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 4.4 years ago by
Robert Castelo
★ 3.3k • written 4.4 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 5.6 years ago by
Gordon Smyth
50k • written 5.6 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 5.7 years ago by
Gordon Smyth
50k • written 5.7 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
5.7 years ago
Andrea Carenzo
• 0
0
votes
1
reply
1.3k
views
GAGE function and the same.dir option
gage
gene set testing
updated 6.0 years ago by
Luo Weijun
★ 1.6k • written 6.0 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 9 days ago by
Chris
▴ 10 • written 7.4 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
7.3 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
7.5 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
50k • written 7.9 years ago by
le2336
▴ 20
1
vote
0
replies
1.3k
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
8.1 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
50k • written 8.5 years ago by
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
9.0 years ago
svlachavas
▴ 830
14 results • Page
1 of 1
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Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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