Showing : gsva • reset
9
votes
7
replies
21k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 13 months ago by ▴ 10 • written 7.5 years ago by ▴ 130
3
votes
9
replies
10k
views
Does GSVA enrichment score comes negative?
GSVA
8.6 years ago • updated 7.7 years ago pbachali ▴ 50
1
vote
3
replies
8.1k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by • 0
12
votes
10
replies
7.9k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
6.8 years ago • updated 6.0 years ago rached ▴ 60
0
votes
8
replies
7.6k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 2.3 years ago by ★ 3.4k • written 3.9 years ago by • 0
1
vote
4
replies
6.2k
views
GSVA on RNAseq data
gsva rnaseq
updated 5.8 years ago by ★ 3.4k • written 5.8 years ago by ▴ 60
0
votes
5
replies
5.6k
views
Convert gene expression matrix to ExpressionSet
GSVA GSVA
updated 13.2 years ago by 25k • written 13.2 years ago by ▴ 360
2
votes
2
replies
5.0k
views
Error in running gsva function from GSVA package
gsva
updated 9.2 years ago by ★ 3.4k • written 9.2 years ago by ▴ 10
0
votes
8
replies
5.0k
views
GSVA: problem with chip annotation
gsva
updated 10.2 years ago by ★ 3.4k • written 10.2 years ago by • 0
2
votes
5
replies
5.0k
views
GSVA error - incomplete instalation?
GSVA ExpressionSet
9.2 years ago • updated 9.1 years ago thrabe • 0
2
votes
10
replies
4.5k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by ▴ 20
0
votes
1
reply
4.0k
views
GSVA Problem
GSVA
updated 3.7 years ago by ★ 3.4k • written 3.7 years ago by • 0
1
vote
2
replies
4.0k
views
GSVA error
GSVA
9 months ago Alex • 0
5
votes
4
replies
3.9k
views
Differential expression on GSVA scores using LIMMA
limma gsva
updated 5.8 years ago by ★ 3.4k • written 5.8 years ago by ▴ 60
2
votes
5
replies
3.7k
views
Problem encountered when running GSVA for RNAseq
gsva rnaseq
updated 10.2 years ago by ★ 3.4k • written 10.2 years ago by • 0
0
votes
9
replies
3.7k
views
problem with using GSVA package
GSVA GSVA
updated 13.2 years ago by ★ 3.4k • written 13.2 years ago by ▴ 360
2
votes
1
reply
3.7k
views
Dealing with the output of ssGSEA method from GSVA package
gsva ssgsea
9.2 years ago Momeneh Foroutan ▴ 10
0
votes
5
replies
3.6k
views
nsFilter error in genefilter
GSVA GSVA
updated 11.8 years ago by ★ 3.4k • written 11.8 years ago by ★ 13k
2
votes
7
replies
3.2k
views
Issue with GSVA using dgCMatrix
GSVA
updated 10 months ago by ▴ 10 • written 3.6 years ago by • 0
0
votes
11
replies
3.2k
views
GSVA: using Entrez ID's as identifiers
probe GSVA probe GSVA
updated 13.2 years ago by ★ 3.4k • written 13.2 years ago by ▴ 360
7
votes
11
replies
3.2k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 60
1
vote
11
replies
3.1k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 3.5 years ago by ▴ 10 • written 4.4 years ago by • 0
1
vote
12
replies
3.0k
views
GSVA (running group samples separately)
GSVA
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 30
2
votes
4
replies
3.0k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4.0 years ago by • 0 • written 5.9 years ago by ▴ 40
4
votes
2
replies
3.0k
views
GSVA: questions about the bootstrap p-value
gsva
updated 7.6 years ago by ★ 3.4k • written 7.6 years ago by ▴ 30
0
votes
3
replies
3.0k
views
[GSVA] Segfault with GSVA
RNASeq Microarray Annotation gcrma convert GSVA RNASeq Microarray Annotation gcrma GSVA
updated 12.0 years ago by ▴ 230 • written 12.0 years ago by ★ 3.4k
8
votes
3
replies
2.9k
views
GSVA indifferent to 'abs.ranking'
GSVA gsva abs.ranking
updated 7.7 years ago by ★ 3.4k • written 7.7 years ago by ▴ 130
0
votes
5
replies
2.9k
views
parallel and GSVA
PROcess GSVA PROcess GSVA
updated 12.0 years ago by ★ 13k • written 12.0 years ago by ▴ 130
0
votes
3
replies
2.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.2 years ago by ▴ 60 • written 2.5 years ago by • 0
5
votes
16
replies
2.8k
views
GSVA package scores are opposite on mac and windows
GSVA bug gsva bugs
updated 7.3 years ago by ★ 3.4k • written 7.3 years ago by ▴ 10
3
votes
4
replies
2.8k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
2.5 years ago Yang Shi ▴ 10
0
votes
5
replies
2.8k
views
GSVA questions
cdf GSVA cdf GSVA
11.4 years ago Guest User ★ 13k
1
vote
2
replies
2.8k
views
GSVA for single sample
gsea gsva ssgsea
6.9 years ago jaison75 ▴ 20
2
votes
1
reply
2.7k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.5 years ago by ★ 3.4k • written 4.5 years ago by ▴ 50
0
votes
5
replies
2.6k
views
GSVA error
GSVA GSVA
updated 12.0 years ago by ★ 3.4k • written 12.0 years ago by ★ 13k
2
votes
6
replies
2.5k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape UCell GSVA
updated 13 months ago by • 0 • written 23 months ago by • 0
4
votes
4
replies
2.5k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea GSVA biotype proteincoding msigdb
updated 3 months ago by • 0 • written 13 months ago by ▴ 200
2
votes
2
replies
2.5k
views
Questions regard to GSVA and Limma
limma GSVA
3.6 years ago Chenxi • 0
2
votes
3
replies
2.4k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4.1 years ago by ★ 3.4k • written 4.1 years ago by ▴ 20
5
votes
9
replies
2.4k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.5 years ago Yang Shi ▴ 10
1
vote
4
replies
2.3k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 6.5 years ago by ★ 3.4k • written 6.5 years ago by • 0
1
vote
1
reply
2.3k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 10
2
votes
2
replies
2.3k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by • 0
2
votes
2
replies
2.2k
views
Input genes for GSVA
gsva gene expression matrix
updated 6.8 years ago by ★ 3.4k • written 6.8 years ago by ▴ 70
4
votes
2
replies
2.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 18 months ago by 52k • written 18 months ago by ▴ 10
1
vote
5
replies
2.1k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
2.2 years ago rocanja ▴ 60
0
votes
2
replies
2.1k
views
Error when running Gene Set Variant Analysis (GSVA)
GSVA GSVA
updated 11.6 years ago by ★ 3.4k • written 11.6 years ago by ▴ 50
6
votes
4
replies
2.1k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.9 years ago hanyin.wang88 ▴ 10
2
votes
4
replies
2.1k
views
Failed to install Biobase
GSVA Biobase
updated 22 months ago by 67k • written 22 months ago by • 0
2
votes
2
replies
2.0k
views
How to run GSVA with partially NA genes
GSVA
2.7 years ago blakebowen • 0
50 results • Page 1 of 1
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Answer: Curiously shaped volcano plot with using oarfish + swish to do differential gene by Michael Love 43k
See swish vignette, these are explained.
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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