Showing : EGSEA • reset
5
votes
6
replies
721
views
EGSEA error during report generation: "only 0's may be mixed with negative subscripts"
EGSEA
updated 7 months ago by • 0 • written 2.0 years ago by ▴ 50
1
vote
0
replies
182
views
EGSEA - clarification of values in the Stats Table
egsea limma
21 months ago rocanja ▴ 60
0
votes
2
replies
419
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA edgeR biomaRt limma RNA-seq
22 months ago fgol ▴ 10
4
votes
6
replies
13k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 3 months ago by • 0 • written 3.9 years ago by ▴ 90
0
votes
1
reply
881
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger dgelist NA egsea
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
vote
0
replies
406
views
EGSEA install licensed KEGG data
EGSEA KEGG EGSEAdata
3.4 years ago john.thompson ▴ 10
0
votes
0
replies
349
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix egsea
3.4 years ago stefano.mangiola • 0
0
votes
5
replies
1.3k
views
EGSEA generateReport() error "no adj nodes"
EGSEA EGSEA123
updated 3.6 years ago by ▴ 40 • written 3.6 years ago by ★ 2.0k
1
vote
1
reply
549
views
EGSEA : unable to plot heatmaps.
EGSEA R bioconductor
3.8 years ago RV • 0
0
votes
2
replies
798
views
Ensemble EGSEA (EGSEA): base GSA method failures
egsea
4.2 years ago irizarnaunk • 0
2
votes
7
replies
851
views
EGSEA - failing to write report
EGSEA write
updated 4.4 years ago by ▴ 40 • written 4.4 years ago by ▴ 20
2
votes
3
replies
848
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
4.5 years ago • updated 4.4 years ago Pekka Kohonen ▴ 190
0
votes
4
replies
914
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 4.7 years ago by ▴ 40 • written 4.7 years ago by • 0
13 results • Page 1 of 1
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Replies
Comment: deseq2 normalized data with heatmap by Ian • 0
Hey @kevin , Thanks for the helpful posts! I noticed in your link to this heatmap analysis, you used scale() and not vst(). However, earli…
Comment: lmFit, continuous exposure, adjustment covariates by AyHi • 0
Dear Gordon, Thank you so much for your reply. It worked well! I just changed y to t because the protein values were included in dat in my…
Answer: To retrieve the transcript from gff file with the longest isoform by James W. MacDonald 57k
Neither biomartr, nor orthologr are Bioconductor packages, so this isn't the place to ask questions about them. However, the question yo…
Comment: Data input for aracne2regulon function in viper package by Mikael • 0
Hi Luna_P, I think I am in a very similar situation. I get the same error message and modified my network file as mentioned above but I s…
Comment: change text size in plotmd functtion by Gordon Smyth 43k
plotMD accepts the usual range of R graphics parameters, see `?par`.
Votes
A: TPM data Differential expression analysis
A: TPM data Differential expression analysis
A: Differential expression of RNA-seq data using limma and voom()
A: Differential expression of RNA-seq data using limma and voom()
Answer: problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignmen
Awards • All
Scholar to Gordon Smyth 43k
Teacher to Guido Hooiveld ★ 3.0k
Scholar to Michael Love 33k
Scholar to Robert Castelo ★ 2.7k
Scholar to James W. MacDonald 57k
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