Showing : gsva • reset
1
vote
2
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201
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GSVA error
GSVA
3 days ago • updated 2 days ago Alex • 0
1
vote
6
replies
420
views
GSVA on separate healthy and disease datasets
GSVA
updated 7 days ago by 65k • written 8 days ago by ▴ 60
1
vote
1
reply
560
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea GSVA biotype proteincoding msigdb
updated 4 months ago by ★ 3.2k • written 4 months ago by ▴ 20
0
votes
1
reply
382
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GSVA exceeds 1
GSVA
updated 7 months ago by ★ 3.2k • written 7 months ago by • 0
3
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2
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1.2k
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Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
2
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0
replies
1.1k
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
12 months ago Tadeoye ▴ 20
0
votes
2
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767
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GSVA with and without absolute scaling method
GSVA
12 months ago arashdeep singh • 0
2
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4
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1.3k
views
Failed to install Biobase
GSVA Biobase
updated 12 months ago by 65k • written 12 months ago by • 0
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 4 months ago by • 0 • written 14 months ago by • 0
0
votes
3
replies
711
views
GSVA: Error loading interactive web app
igsva GSVA
updated 14 months ago by ★ 3.2k • written 14 months ago by ▴ 40
0
votes
3
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1.0k
views
GSVA results interpretation
GSVA
updated 15 months ago by ★ 3.2k • written 15 months ago by • 0
0
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0
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699
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
15 months ago Zhijie • 0
0
votes
0
replies
745
views
Job: Research software engineer at UPF Barcelona
JobPosting Devel GSVA Software
17 months ago Robert Castelo ★ 3.2k
1
vote
5
replies
1.5k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
17 months ago rocanja ▴ 60
5
votes
9
replies
1.8k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 months ago • updated 20 months ago Yang Shi ▴ 10
3
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4
replies
2.0k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
21 months ago Yang Shi ▴ 10
0
votes
3
replies
1.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 17 months ago by ▴ 60 • written 21 months ago by • 0
1
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2
replies
1.1k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
2.6 years ago • updated 22 months ago Guandong Shang ▴ 40
2
votes
2
replies
1.3k
views
How to run GSVA with partially NA genes
GSVA
23 months ago blakebowen • 0
1
vote
3
replies
5.3k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.0 years ago by ★ 3.2k • written 2.0 years ago by • 0
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.1 years ago by ★ 3.2k • written 2.1 years ago by • 0
0
votes
1
reply
771
views
Running PLAGE gets killed
GSVA SingleCellData
updated 2.1 years ago by ★ 3.2k • written 2.1 years ago by • 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 ★ 3.2k • written 2.1 years ago by • 0
0
votes
1
reply
1.2k
views
GSVA package normalization on gene-length ?
GSVA
updated 2.3 years ago by ★ 3.2k • written 2.3 years ago by • 0
1
vote
11
replies
2.6k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 2.7 years ago by ▴ 10 • written 3.7 years ago by • 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
823
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.8 years ago k.vitting.seerup ▴ 120
2
votes
7
replies
1.7k
views
Issue with GSVA using dgCMatrix
GSVA
updated 6 weeks ago by ▴ 10 • written 2.8 years ago by • 0
0
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1
reply
3.0k
views
GSVA Problem
GSVA
updated 2.9 years ago by ★ 3.2k • written 2.9 years ago by • 0
6
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4
replies
1.7k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.2 years ago hanyin.wang88 ▴ 10
0
votes
8
replies
5.5k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 19 months ago by ★ 3.2k • written 3.2 years ago by • 0
2
votes
3
replies
1.8k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.3 years ago by ★ 3.2k • written 3.3 years ago by ▴ 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 ★ 3.2k • written 3.5 years ago by ▴ 70
0
votes
1
reply
1.1k
views
Extract GSVA gene rank matrix
gsva
updated 3.7 years ago by ★ 3.2k • written 3.7 years ago by • 0
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.2k • written 3.8 years ago by ▴ 40
2
votes
2
replies
1.8k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 3.8 years ago by ★ 3.2k • written 3.8 years ago by • 0
2
votes
10
replies
3.6k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 3.8 years ago by ★ 3.2k • written 3.8 years ago by ▴ 20
0
votes
1
reply
1.5k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA Job
updated 3.9 years ago by ★ 3.2k • written 3.9 years ago by • 0
1
vote
12
replies
2.4k
views
GSVA (running group samples separately)
GSVA
updated 3.9 years ago by ★ 3.2k • written 3.9 years ago by ▴ 30
7
votes
11
replies
2.3k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by ▴ 60
1
vote
1
reply
1.7k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by ▴ 10
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 4 months ago by ▴ 10 • written 6.7 years ago by ▴ 130
1
vote
4
replies
4.9k
views
GSVA on RNAseq data
gsva rnaseq
updated 5.0 years ago by ★ 3.2k • written 5.0 years ago by ▴ 60
0
votes
1
reply
930
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 5.0 years ago by ★ 3.2k • written 5.0 years ago by ▴ 10
1
vote
1
reply
1.4k
views
GSVA with NanoString nCounter data
GSVA Nanostring
5.8 years ago • updated 5.0 years ago SB • 0
5
votes
4
replies
3.0k
views
Differential expression on GSVA scores using LIMMA
limma gsva
updated 5.0 years ago by ★ 3.2k • written 5.0 years ago by ▴ 60
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 • 0 • written 5.1 years ago by ▴ 40
12
votes
10
replies
6.4k
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 5.2 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
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
5.3 years ago krassowski.michal ▴ 40
50 results • Page 1 of 1
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Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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