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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
3.5 years ago
svlachavas
▴ 830
4
votes
11
replies
1.9k
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 4.3 years ago by
Robert Castelo
★ 3.1k • written 4.3 years ago by
Jeremy Beales
▴ 10
2
votes
3
replies
1.3k
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 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
svlachavas
▴ 830
7
votes
2
replies
1.3k
views
Pre-ranked camera gene set testing with edgeR results
limma
camera
cameraPR
edgeR
gene set testing
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
jamie.gearing
▴ 60
1
vote
4
replies
1.2k
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
5.6 years ago
Andrea Carenzo
• 0
0
votes
1
reply
1.3k
views
GAGE function and the same.dir option
gage
gene set testing
updated 5.8 years ago by
Luo Weijun
★ 1.6k • written 5.8 years ago by
Aurora
▴ 20
2
votes
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
7.2 years ago • updated 7.1 years ago
Pekka Kohonen
▴ 190
4
votes
6
replies
1.9k
views
Gene set Testing with Limma for Agilent IDs probes?
limma
agilent microarrays
gene set testing
annotation
7.2 years ago
Bouzid.a
▴ 20
7
votes
13
replies
2.1k
views
Test whether expression levels of two gene sets are significantly different
R
DESeq2
gene set testing
gene expression
7.4 years ago • updated 7.3 years ago
Jon Bråte
▴ 250
3
votes
4
replies
1.5k
views
Competitive gene set testing between two sets of genes
gene set testing
camera
edger
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 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
7.9 years ago
m.fletcher
▴ 20
1
vote
5
replies
2.0k
views
Confused by results from CAMERA gene set testing
limma
camera
gene set testing
7.9 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 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
svlachavas
▴ 830
6
votes
10
replies
1.7k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing
roast
mroast
differential gene expression
bioconductor
8.8 years ago
svlachavas
▴ 830
14 results • Page
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
If you include `0+` in the model formula, then the order of the batch and treatment factors in the model becomes important. You need `0+gro…
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
by
James W. MacDonald
65k
The main goal here is to map human gene symbols to something else, which you can use the `Orthology.eg.db` package to do. You could also us…
Comment: How can I compute AIC for MAST hurdle model fitted in the whole dataset?
by
rproendo
▴ 20
Hi OP, checking in to see if you found a solution to this issue. I'm also interested in using AICs to evaluate model fits in MAST.
Comment: padj-based gradient scale from barplot (clusterProfiler results) does not work p
by
Eva
▴ 10
Oh god, it is right, how I didn't realise before. I got confused with the scientific format of the numbers and I was in a loop for nothing.…
Comment: Downloading count matrix for full recount3 dataset
by
Leonardo Collado Torres
★ 1.0k
AFAIK it's not.
Votes
A: HLA genes missing from TxDb.Hsapiens.UCSC.hg38.knownGene
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
DESeq2 design with multiple factors
A: Three-factor design with DESeq2
A: DESeq2: multiple factors and comparison of a main factor between samples
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