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gsva
•
reset
4
votes
5
replies
341
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
15 days ago • updated 5 days ago
Chris
▴ 10
0
votes
0
replies
97
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago
Chris
▴ 10
1
vote
2
replies
729
views
GSVA error
GSVA
5 weeks ago
Alex
• 0
1
vote
6
replies
526
views
GSVA on separate healthy and disease datasets
GSVA
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
Lucy
▴ 60
1
vote
1
reply
698
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
424
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
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 10 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
13 months ago
Tadeoye
▴ 20
0
votes
2
replies
807
views
GSVA with and without absolute scaling method
GSVA
13 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
66k • written 13 months ago by
johann.brisseau
• 0
2
votes
6
replies
1.7k
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 15 months ago by
Omer
• 0
0
votes
3
replies
767
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 15 months ago by
Robert Castelo
★ 3.3k • written 15 months ago by
sharvari gujja
▴ 40
0
votes
3
replies
1.1k
views
GSVA results interpretation
GSVA
updated 16 months ago by
Robert Castelo
★ 3.3k • written 16 months ago by
munta.jihad
• 0
0
votes
0
replies
755
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
801
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
18 months ago
Robert Castelo
★ 3.3k
1
vote
5
replies
1.6k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
18 months ago
rocanja
▴ 60
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
22 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
0
votes
3
replies
2.0k
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
2
votes
2
replies
1.4k
views
How to run GSVA with partially NA genes
GSVA
24 months ago
blakebowen
• 0
1
vote
3
replies
5.6k
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
1.3k
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
814
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 2.2 years ago by
Robert Castelo
★ 3.3k • written 2.2 years ago by
Amna
• 0
0
votes
1
reply
1.3k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata
GSVA
updated 2.2 years ago by
Robert Castelo
★ 3.3k • written 2.2 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
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
852
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.9 years ago
k.vitting.seerup
▴ 120
2
votes
2
replies
2.0k
views
Questions regard to GSVA and Limma
limma
GSVA
2.9 years ago
Chenxi
• 0
2
votes
7
replies
1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 10 weeks ago by
Moritz
▴ 10 • written 2.9 years ago by
resa
• 0
0
votes
1
reply
3.1k
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
3.3 years ago
hanyin.wang88
▴ 10
0
votes
8
replies
5.8k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 20 months ago by
Robert Castelo
★ 3.3k • written 3.3 years ago by
Siyuan
• 0
2
votes
3
replies
1.9k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.4 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 3.6 years ago by
Robert Castelo
★ 3.3k • written 3.6 years ago by
Endre Sebestyén
▴ 70
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
1
reply
1.2k
views
Extract GSVA gene rank matrix
gsva
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
dylan
• 0
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 years ago by
igor
▴ 50
2
votes
2
replies
1.9k
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
3.8k
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 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 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
2.5k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.1 years ago by
Robert Castelo
★ 3.3k • written 4.1 years ago by
rocanja
▴ 60
1
vote
1
reply
1.8k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.1 years ago by
Robert Castelo
★ 3.3k • written 4.1 years ago by
thkapell
▴ 10
1
vote
4
replies
5.1k
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
959
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
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
2
votes
4
replies
2.5k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 3.4 years ago by
Dharmesh D Bhuva
• 0 • written 5.2 years ago by
Pietro
▴ 40
0
votes
0
replies
1.1k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA
geneset
RNASeq
TCGA
subtypes
5.4 years ago
Pietro
▴ 40
1
vote
1
reply
1.3k
views
PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva
plage
differential expression
gene set enrichment
5.4 years ago
krassowski.michal
▴ 40
2
votes
1
reply
1.2k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 5.7 years ago by
Robert Castelo
★ 3.3k • written 5.7 years ago by
owen.whitley
▴ 10
50 results • Page
1 of 1
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Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
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