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EGSEA
•
reset
3
votes
5
replies
914
views
Help with running egsea()
EGSEA
11 months ago
Chris
▴ 20
0
votes
1
reply
550
views
EGSEA with Affymetrix data
EGSEA
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
cverschoor
• 0
0
votes
1
reply
699
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA
EGSEAdata
EGSEA123
DifferentialExpression
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Tiago
• 0
0
votes
1
reply
1.1k
views
EGSEA::egsea - Parallelization issue and "Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : negative length vectors are not allowed"
egsea
EGSEA123
2.0 years ago
neilzhao
▴ 30
0
votes
3
replies
2.9k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 2.8 years ago by
shepherl
4.1k • written 2.8 years ago by
Jenny Drnevich
★ 2.0k
6
votes
6
replies
3.6k
views
EGSEA error during report generation: "only 0's may be mixed with negative subscripts"
EGSEA
updated 4.5 years ago by
Martin
• 0 • written 5.8 years ago by
pgugger
▴ 70
1
vote
0
replies
930
views
EGSEA - clarification of values in the Stats Table
egsea
limma
5.6 years ago
rocanja
▴ 60
0
votes
2
replies
1.6k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA
edgeR
biomaRt
limma
RNA-seq
5.7 years ago
fgol
▴ 10
9
votes
7
replies
22k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 16 months ago by
amin8w
▴ 10 • written 7.8 years ago by
sina.nassiri
▴ 130
0
votes
1
reply
2.6k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.2 years ago by
Gordon Smyth
52k • written 7.2 years ago by
belmore
• 0
1
vote
0
replies
1.3k
views
EGSEA install licensed KEGG data
EGSEA
KEGG
EGSEAdata
7.2 years ago
john.thompson
▴ 10
0
votes
0
replies
1.1k
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix
egsea
7.2 years ago
Stefano Mangiola
▴ 40
0
votes
5
replies
3.1k
views
EGSEA generateReport() error "no adj nodes"
EGSEA
EGSEA123
updated 7.4 years ago by
Monther Alhamdoosh
▴ 40 • written 7.4 years ago by
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.4k
views
EGSEA : unable to plot heatmaps.
EGSEA
R bioconductor
7.6 years ago
RV
• 0
0
votes
2
replies
1.8k
views
Ensemble EGSEA (EGSEA): base GSA method failures
egsea
8.0 years ago
irizarnaunk
• 0
2
votes
7
replies
2.3k
views
EGSEA - failing to write report
EGSEA
write
updated 8.2 years ago by
Monther Alhamdoosh
▴ 40 • written 8.2 years ago by
mforde84
▴ 20
2
votes
4
replies
2.1k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 11 months ago by
Chris
▴ 20 • written 8.3 years ago by
Pekka Kohonen
▴ 190
0
votes
4
replies
2.4k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways
gsea
egsea
gage
updated 8.6 years ago by
Monther Alhamdoosh
▴ 40 • written 8.6 years ago by
yingchen
• 0
18 results • Page
1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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