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gsva
•
reset
0
votes
0
replies
55
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
1
vote
2
replies
486
views
GSVA error
GSVA
18 days ago • updated 17 days ago
Alex
• 0
1
vote
6
replies
481
views
GSVA on separate healthy and disease datasets
GSVA
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
Lucy
▴ 60
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
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
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
1
reply
624
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 5 months ago by
Robert Castelo
★ 3.3k • written 5 months ago by
snijesh
▴ 20
0
votes
1
reply
403
views
GSVA exceeds 1
GSVA
updated 8 months ago by
Robert Castelo
★ 3.3k • written 8 months ago by
Heba
• 0
4
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 9 months ago by
Gordon Smyth
50k • written 10 months ago by
Jonathan
▴ 10
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
12 months ago
Tadeoye
▴ 20
0
votes
2
replies
786
views
GSVA with and without absolute scaling method
GSVA
12 months ago
arashdeep singh
• 0
2
votes
4
replies
1.4k
views
Failed to install Biobase
GSVA
Biobase
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
johann.brisseau
• 0
0
votes
3
replies
742
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 14 months ago by
Robert Castelo
★ 3.3k • written 14 months ago by
sharvari gujja
▴ 40
0
votes
3
replies
1.1k
views
GSVA results interpretation
GSVA
updated 15 months ago by
Robert Castelo
★ 3.3k • written 15 months ago by
munta.jihad
• 0
0
votes
0
replies
729
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
16 months ago
Zhijie
• 0
0
votes
0
replies
770
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
17 months ago
Robert Castelo
★ 3.3k
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
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
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
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
3
votes
4
replies
2.1k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
22 months ago
Yang Shi
▴ 10
1
vote
2
replies
1.1k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
2.7 years ago • updated 23 months ago
Guandong Shang
▴ 40
2
votes
2
replies
1.4k
views
How to run GSVA with partially NA genes
GSVA
23 months ago
blakebowen
• 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
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
forlani.luca
• 0
0
votes
1
reply
787
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
Amna
• 0
0
votes
1
reply
1.2k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
random
• 0
0
votes
1
reply
1.2k
views
GSVA package normalization on gene-length ?
GSVA
updated 2.4 years ago by
Robert Castelo
★ 3.3k • written 2.4 years ago by
xanthexu
• 0
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
2
votes
2
replies
2.0k
views
Questions regard to GSVA and Limma
limma
GSVA
2.8 years ago
Chenxi
• 0
2
votes
2
replies
839
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.8 years ago
k.vitting.seerup
▴ 120
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
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
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
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
0
votes
3
replies
1.4k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 3.5 years ago by
Robert Castelo
★ 3.3k • written 3.5 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.1k
views
Extract GSVA gene rank matrix
gsva
updated 3.7 years ago by
Robert Castelo
★ 3.3k • written 3.7 years ago by
dylan
• 0
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
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
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
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
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
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
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
1
reply
945
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 5.1 years ago by
Robert Castelo
★ 3.3k • written 5.1 years ago by
owen.whitley
▴ 10
1
vote
1
reply
1.4k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.1 years ago
SB
• 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
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
0
replies
1.0k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA
geneset
RNASeq
TCGA
subtypes
5.3 years ago
Pietro
▴ 40
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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