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gsva
•
reset
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 5 months ago by
amin8w
▴ 10 • written 6.8 years ago by
sina.nassiri
▴ 130
3
votes
9
replies
8.8k
views
Does GSVA enrichment score comes negative?
GSVA
7.8 years ago • updated 7.0 years ago
pbachali
▴ 50
12
votes
10
replies
6.6k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.1 years ago • updated 5.3 years ago
rached
▴ 60
0
votes
8
replies
5.6k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 19 months ago by
Robert Castelo
★ 3.3k • written 3.2 years ago by
Siyuan
• 0
1
vote
3
replies
5.4k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
Davide
• 0
0
votes
5
replies
5.2k
views
Convert gene expression matrix to ExpressionSet
GSVA
GSVA
updated 12.5 years ago by
Martin Morgan
25k • written 12.5 years ago by
Wendy Qiao
▴ 360
1
vote
4
replies
5.0k
views
GSVA on RNAseq data
gsva
rnaseq
updated 5.1 years ago by
Robert Castelo
★ 3.3k • written 5.1 years ago by
rocanja
▴ 60
0
votes
8
replies
4.2k
views
GSVA: problem with chip annotation
gsva
updated 9.5 years ago by
Robert Castelo
★ 3.3k • written 9.5 years ago by
q017mm
• 0
2
votes
5
replies
3.9k
views
GSVA error - incomplete instalation?
GSVA
ExpressionSet
8.5 years ago • updated 8.4 years ago
thrabe
• 0
2
votes
10
replies
3.7k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 years ago by
hsiowa2
▴ 20
2
votes
2
replies
3.5k
views
Error in running gsva function from GSVA package
gsva
updated 8.5 years ago by
Robert Castelo
★ 3.3k • written 8.5 years ago by
Momeneh Foroutan
▴ 10
0
votes
5
replies
3.3k
views
nsFilter error in genefilter
GSVA
GSVA
updated 11.0 years ago by
Robert Castelo
★ 3.3k • written 11.0 years ago by
Guest User
★ 13k
2
votes
1
reply
3.3k
views
Dealing with the output of ssGSEA method from GSVA package
gsva
ssgsea
8.5 years ago
Momeneh Foroutan
▴ 10
2
votes
5
replies
3.2k
views
Problem encountered when running GSVA for RNAseq
gsva
rnaseq
updated 9.5 years ago by
Robert Castelo
★ 3.3k • written 9.5 years ago by
polly0806
• 0
5
votes
4
replies
3.1k
views
Differential expression on GSVA scores using LIMMA
limma
gsva
updated 5.1 years ago by
Robert Castelo
★ 3.3k • written 5.1 years ago by
rocanja
▴ 60
0
votes
1
reply
3.0k
views
GSVA Problem
GSVA
updated 3.0 years ago by
Robert Castelo
★ 3.3k • written 3.0 years ago by
tywzlzl2011
• 0
0
votes
9
replies
2.9k
views
problem with using GSVA package
GSVA
GSVA
updated 12.5 years ago by
Robert Castelo
★ 3.3k • written 12.5 years ago by
Wendy Qiao
▴ 360
0
votes
11
replies
2.9k
views
GSVA: using Entrez ID's as identifiers
probe
GSVA
probe
GSVA
updated 12.5 years ago by
Robert Castelo
★ 3.3k • written 12.5 years ago by
Wendy Qiao
▴ 360
1
vote
11
replies
2.7k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 2.8 years ago by
soudayo
▴ 10 • written 3.7 years ago by
yaoxucpu
• 0
0
votes
3
replies
2.7k
views
[GSVA] Segfault with GSVA
RNASeq
Microarray
Annotation
gcrma
convert
GSVA
RNASeq
Microarray
Annotation
gcrma
GSVA
updated 11.3 years ago by
capricy gao
▴ 230 • written 11.3 years ago by
Robert Castelo
★ 3.3k
0
votes
5
replies
2.6k
views
parallel and GSVA
PROcess
GSVA
PROcess
GSVA
updated 11.3 years ago by
Steve Lianoglou
★ 13k • written 11.3 years ago by
David Iles
▴ 130
4
votes
2
replies
2.6k
views
GSVA: questions about the bootstrap p-value
gsva
updated 6.9 years ago by
Robert Castelo
★ 3.3k • written 6.9 years ago by
dionnezaal
▴ 30
0
votes
5
replies
2.5k
views
GSVA questions
cdf
GSVA
cdf
GSVA
10.7 years ago
Guest User
★ 13k
8
votes
3
replies
2.4k
views
GSVA indifferent to 'abs.ranking'
GSVA
gsva
abs.ranking
updated 7.0 years ago by
Robert Castelo
★ 3.3k • written 7.0 years ago by
sina.nassiri
▴ 130
2
votes
4
replies
2.4k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 3.3 years ago by
Dharmesh D Bhuva
• 0 • written 5.1 years ago by
Pietro
▴ 40
1
vote
12
replies
2.4k
views
GSVA (running group samples separately)
GSVA
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
Jenn
▴ 30
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
rocanja
▴ 60
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea
gsva
ssgsea
6.2 years ago
jaison75
▴ 20
5
votes
16
replies
2.3k
views
GSVA package scores are opposite on mac and windows
GSVA
bug
gsva
bugs
updated 6.6 years ago by
Robert Castelo
★ 3.3k • written 6.6 years ago by
JasonL_Weirather
▴ 10
0
votes
5
replies
2.1k
views
GSVA error
GSVA
GSVA
updated 11.2 years ago by
Robert Castelo
★ 3.3k • written 11.2 years ago by
Guest User
★ 13k
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
igor
▴ 40
3
votes
4
replies
2.1k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
22 months ago
Yang Shi
▴ 10
2
votes
2
replies
2.0k
views
Questions regard to GSVA and Limma
limma
GSVA
2.8 years ago
Chenxi
• 0
1
vote
4
replies
2.0k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 5.8 years ago by
Robert Castelo
★ 3.3k • written 5.8 years ago by
Shi-Xiang Wang
• 0
0
votes
2
replies
1.9k
views
Error when running Gene Set Variant Analysis (GSVA)
GSVA
GSVA
updated 10.9 years ago by
Robert Castelo
★ 3.3k • written 10.9 years ago by
Lucas Santana dos Santos
▴ 50
0
votes
3
replies
1.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 18 months ago by
rocanja
▴ 60 • written 22 months ago by
João
• 0
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
21 months ago
Yang Shi
▴ 10
2
votes
2
replies
1.8k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 years ago by
initialqy
• 0
2
votes
2
replies
1.8k
views
Input genes for GSVA
gsva
gene expression matrix
updated 6.0 years ago by
Robert Castelo
★ 3.3k • written 6.1 years ago by
CodeAway
▴ 70
2
votes
3
replies
1.8k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.3 years ago by
Robert Castelo
★ 3.3k • written 3.4 years ago by
hsiowa2
▴ 20
2
votes
7
replies
1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 8 weeks ago by
Moritz
▴ 10 • written 2.9 years ago by
resa
• 0
6
votes
4
replies
1.8k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.2 years ago
hanyin.wang88
▴ 10
1
vote
1
reply
1.7k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
thkapell
▴ 10
0
votes
2
replies
1.7k
views
Problem in running GSVA
GSVA
getting error in gsva function
9.3 years ago
sathyabaarathi
• 0
0
votes
1
reply
1.7k
views
nsFilter error in genefilter
GO
hgu133plus2
cdf
GSVA
AnnotationForge
GO
hgu133plus2
cdf
GSVA
AnnotationForge
updated 10.8 years ago by
James W. MacDonald
65k • written 10.8 years ago by
steven wink
▴ 90
2
votes
6
replies
1.6k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 5 months ago by
arina
• 0 • written 14 months ago by
Omer
• 0
1
vote
0
replies
1.6k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq
rna-seq
preprocessing
gsva
7.7 years ago
t.kuilman
▴ 170
0
votes
3
replies
1.5k
views
about running gsva on mac
PROcess
GSVA
PROcess
GSVA
updated 10.8 years ago by
Devon Ryan
▴ 200 • written 10.8 years ago by
Ed
▴ 230
1
vote
5
replies
1.5k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
18 months ago • updated 17 months ago
rocanja
▴ 60
0
votes
1
reply
1.5k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 years ago by
laura.derooij
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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