Showing : egsea • reset
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 4 months ago by ▴ 10 • written 6.7 years ago by ▴ 130
6
votes
6
replies
2.8k
views
EGSEA error during report generation: "only 0's may be mixed with negative subscripts"
EGSEA
updated 3.5 years ago by • 0 • written 4.8 years ago by ▴ 70
2
votes
7
replies
1.8k
views
EGSEA - failing to write report
EGSEA write
updated 7.2 years ago by ▴ 40 • written 7.2 years ago by ▴ 20
2
votes
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
7.3 years ago • updated 7.2 years ago Pekka Kohonen ▴ 190
1
vote
1
reply
1.1k
views
EGSEA : unable to plot heatmaps.
EGSEA R bioconductor
6.6 years ago RV • 0
1
vote
0
replies
984
views
EGSEA install licensed KEGG data
EGSEA KEGG EGSEAdata
6.2 years ago john.thompson ▴ 10
1
vote
0
replies
711
views
EGSEA - clarification of values in the Stats Table
egsea limma
4.6 years ago rocanja ▴ 60
0
votes
1
reply
265
views
EGSEA with Affymetrix data
EGSEA
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
3
replies
1.9k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 22 months ago by 3.8k • written 22 months ago by ★ 2.0k
0
votes
4
replies
1.9k
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 7.6 years ago by ▴ 40 • written 7.6 years ago by • 0
0
votes
1
reply
739
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
12 months ago neilzhao ▴ 30
0
votes
2
replies
1.5k
views
Ensemble EGSEA (EGSEA): base GSA method failures
egsea
7.0 years ago irizarnaunk • 0
0
votes
5
replies
2.6k
views
EGSEA generateReport() error "no adj nodes"
EGSEA EGSEA123
updated 6.4 years ago by ▴ 40 • written 6.4 years ago by ★ 2.0k
0
votes
0
replies
840
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix egsea
6.2 years ago Stefano Mangiola ▴ 10
0
votes
1
reply
2.2k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger dgelist NA egsea
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
0
votes
2
replies
1.3k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA edgeR biomaRt limma RNA-seq
4.6 years ago fgol ▴ 10
0
votes
1
reply
362
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 7 months ago by 65k • written 7 months ago by • 0
17 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards • All
Scholar to Robert Castelo ★ 3.2k
Popular Question to James W. MacDonald 65k
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Popular Question to Gordon Smyth 50k
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