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gsva
•
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1
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363
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GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 3 days ago by
ATpoint
★ 4.7k • written 3 days ago by
amien.vp
• 0
5
votes
4
replies
879
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 27 days ago by
Axel Klenk
★ 1.1k • written 4 weeks ago by
1sunmic2
• 0
1
vote
2
replies
601
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
11 weeks ago
georgii.vdovin
• 0
0
votes
5
replies
627
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 3 months ago by
Kent
• 0
1
vote
4
replies
1.4k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 4 months ago by
Tyler Sagendorf
▴ 10 • written 5 months ago by
Bob
▴ 10
0
votes
1
reply
1.2k
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
written 2.3 years ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
650
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 6 months ago by
Axel Klenk
★ 1.1k • written 6 months ago by
Bioinformagician
• 0
1
vote
4
replies
1.7k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
7 months ago
Lucy
▴ 60
1
vote
1
reply
616
views
GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
updated 8 months ago by
Axel Klenk
★ 1.1k • written 8 months ago by
johanna.galvis
• 0
1
vote
2
replies
607
views
Interpretation of GSVA with absRanking=TRUE
GSVA
9 months ago • updated 8 months ago
gad.abraham
• 0
0
votes
3
replies
1.2k
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 9 months ago by
Robert Castelo
★ 3.4k • written 9 months ago by
michelafrancesconi8
• 0
4
votes
5
replies
1.4k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
10 months ago • updated 9 months ago
Chris
▴ 20
0
votes
0
replies
428
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
10 months ago
Chris
▴ 20
1
vote
2
replies
4.6k
views
GSVA error
GSVA
10 months ago
Alex
• 0
1
vote
6
replies
1.1k
views
GSVA on separate healthy and disease datasets
GSVA
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Lucy
▴ 60
4
votes
4
replies
3.1k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 5 months ago by
tifaGis
• 0 • written 15 months ago by
snijesh
▴ 200
0
votes
1
reply
718
views
GSVA exceeds 1
GSVA
updated 18 months ago by
Robert Castelo
★ 3.4k • written 18 months ago by
Heba
• 0
4
votes
2
replies
2.4k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 20 months ago by
Gordon Smyth
52k • written 20 months ago by
Jonathan
▴ 10
2
votes
0
replies
2.0k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
23 months ago
Tadeoye
▴ 20
0
votes
2
replies
1.2k
views
GSVA with and without absolute scaling method
GSVA
23 months ago
arashdeep singh
• 0
2
votes
4
replies
2.2k
views
Failed to install Biobase
GSVA
Biobase
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
johann.brisseau
• 0
2
votes
6
replies
2.7k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 15 months ago by
arina
• 0 • written 2.0 years ago by
Omer
• 0
0
votes
3
replies
1.2k
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 2.0 years ago by
Robert Castelo
★ 3.4k • written 2.1 years ago by
sharvari gujja
▴ 40
0
votes
3
replies
2.1k
views
GSVA results interpretation
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.4k • written 2.1 years ago by
munta.jihad
• 0
0
votes
0
replies
1.2k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
2.2 years ago
Zhijie
• 0
1
vote
5
replies
2.3k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
2.3 years ago
rocanja
▴ 60
5
votes
9
replies
2.5k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
2.6 years ago
Yang Shi
▴ 10
3
votes
4
replies
2.9k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
2.7 years ago
Yang Shi
▴ 10
0
votes
3
replies
3.1k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 2.3 years ago by
rocanja
▴ 60 • written 2.7 years ago by
João
• 0
1
vote
2
replies
1.6k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
3.5 years ago • updated 2.7 years ago
Guandong Shang
▴ 40
2
votes
2
replies
2.1k
views
How to run GSVA with partially NA genes
GSVA
2.8 years ago
blakebowen
• 0
1
vote
3
replies
8.7k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.9 years ago by
Robert Castelo
★ 3.4k • written 2.9 years ago by
Davide
• 0
1
vote
1
reply
2.0k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.9 years ago by
Robert Castelo
★ 3.4k • written 2.9 years ago by
forlani.luca
• 0
0
votes
1
reply
1.1k
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 3.0 years ago by
Robert Castelo
★ 3.4k • written 3.0 years ago by
Amna
• 0
0
votes
1
reply
1.8k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata
GSVA
updated 3.0 years ago by
Robert Castelo
★ 3.4k • written 3.0 years ago by
random
• 0
0
votes
1
reply
1.8k
views
GSVA package normalization on gene-length ?
GSVA
updated 3.2 years ago by
Robert Castelo
★ 3.4k • written 3.2 years ago by
xanthexu
• 0
1
vote
11
replies
3.2k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 3.6 years ago by
soudayo
▴ 10 • written 4.5 years ago by
yaoxucpu
• 0
2
votes
2
replies
2.6k
views
Questions regard to GSVA and Limma
limma
GSVA
3.7 years ago
Chenxi
• 0
2
votes
2
replies
1.1k
views
Turn of GSVA filtering for method ssGSEA
GSVA
3.7 years ago
k.vitting.seerup
▴ 120
2
votes
7
replies
3.6k
views
Issue with GSVA using dgCMatrix
GSVA
updated 12 months ago by
Moritz
▴ 10 • written 3.7 years ago by
resa
• 0
0
votes
1
reply
4.3k
views
GSVA Problem
GSVA
updated 3.8 years ago by
Robert Castelo
★ 3.4k • written 3.8 years ago by
tywzlzl2011
• 0
6
votes
4
replies
2.2k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
4.1 years ago • updated 4.0 years ago
hanyin.wang88
▴ 10
0
votes
8
replies
8.0k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 2.4 years ago by
Robert Castelo
★ 3.4k • written 4.1 years ago by
Siyuan
• 0
2
votes
3
replies
2.6k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4.2 years ago by
Robert Castelo
★ 3.4k • written 4.2 years ago by
hsiowa2
▴ 20
0
votes
3
replies
2.0k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 4.3 years ago by
Robert Castelo
★ 3.4k • written 4.4 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.5k
views
Extract GSVA gene rank matrix
gsva
updated 4.6 years ago by
Robert Castelo
★ 3.4k • written 4.6 years ago by
dylan
• 0
2
votes
1
reply
2.9k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 4.6 years ago by
Robert Castelo
★ 3.4k • written 4.6 years ago by
igor
▴ 50
2
votes
2
replies
2.4k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 4.7 years ago by
Robert Castelo
★ 3.4k • written 4.7 years ago by
initialqy
• 0
2
votes
10
replies
4.6k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 4.7 years ago by
Robert Castelo
★ 3.4k • written 4.7 years ago by
hsiowa2
▴ 20
0
votes
1
reply
1.9k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 4.8 years ago by
Robert Castelo
★ 3.4k • written 4.8 years ago by
laura.derooij
• 0
50 results • Page
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Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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