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egsea
•
reset
3
votes
5
replies
1.0k
views
Help with running egsea()
EGSEA
16 months ago
Chris
▴ 20
0
votes
1
reply
614
views
EGSEA with Affymetrix data
EGSEA
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
cverschoor
• 0
0
votes
1
reply
770
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA
EGSEAdata
EGSEA123
DifferentialExpression
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Tiago
• 0
0
votes
1
reply
1.2k
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
2.4 years ago
neilzhao
▴ 30
0
votes
3
replies
3.0k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 3.2 years ago by
shepherl
4.2k • written 3.2 years ago by
Jenny Drnevich
★ 2.0k
6
votes
6
replies
3.7k
views
EGSEA error during report generation: "only 0's may be mixed with negative subscripts"
EGSEA
updated 4.8 years ago by
Martin
• 0 • written 6.2 years ago by
pgugger
▴ 70
1
vote
0
replies
982
views
EGSEA - clarification of values in the Stats Table
egsea
limma
6.0 years ago
rocanja
▴ 60
0
votes
2
replies
1.7k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA
edgeR
biomaRt
limma
RNA-seq
6.0 years ago
fgol
▴ 10
9
votes
7
replies
22k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 21 months ago by
amin8w
▴ 10 • written 8.1 years ago by
sina.nassiri
▴ 130
0
votes
1
reply
2.7k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
belmore
• 0
1
vote
0
replies
1.4k
views
EGSEA install licensed KEGG data
EGSEA
KEGG
EGSEAdata
7.6 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
7.6 years ago
Stefano Mangiola
▴ 40
0
votes
5
replies
3.2k
views
EGSEA generateReport() error "no adj nodes"
EGSEA
EGSEA123
updated 7.8 years ago by
Monther Alhamdoosh
▴ 40 • written 7.8 years ago by
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.5k
views
EGSEA : unable to plot heatmaps.
EGSEA
R bioconductor
8.0 years ago
RV
• 0
0
votes
2
replies
1.9k
views
Ensemble EGSEA (EGSEA): base GSA method failures
egsea
8.4 years ago
irizarnaunk
• 0
2
votes
7
replies
2.4k
views
EGSEA - failing to write report
EGSEA
write
updated 8.6 years ago by
Monther Alhamdoosh
▴ 40 • written 8.6 years ago by
mforde84
▴ 20
2
votes
4
replies
2.2k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 16 months ago by
Chris
▴ 20 • written 8.7 years ago by
Pekka Kohonen
▴ 190
0
votes
4
replies
2.5k
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 8.9 years ago by
Monther Alhamdoosh
▴ 40 • written 8.9 years ago by
yingchen
• 0
18 results • Page
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Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel
by
James W. MacDonald
68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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