Showing : gsva • reset
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GSVA: problem with chip annotation
gsva
updated 9.5 years ago by ★ 3.3k • written 9.5 years ago by • 0
2
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5
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3.2k
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Problem encountered when running GSVA for RNAseq
gsva rnaseq
updated 9.5 years ago by ★ 3.3k • written 9.5 years ago by • 0
3
votes
9
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Does GSVA enrichment score comes negative?
GSVA
7.9 years ago • updated 7.0 years ago pbachali ▴ 50
2
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5
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3.9k
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GSVA error - incomplete instalation?
GSVA ExpressionSet
8.5 years ago • updated 8.4 years ago thrabe • 0
0
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5
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3.3k
views
nsFilter error in genefilter
GSVA GSVA
updated 11.1 years ago by ★ 3.3k • written 11.1 years ago by ★ 13k
0
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3
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1.5k
views
about running gsva on mac
PROcess GSVA PROcess GSVA
updated 10.8 years ago by ▴ 200 • written 10.8 years ago by ▴ 230
1
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11
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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 ▴ 10 • written 3.7 years ago by • 0
0
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2
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1.7k
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Problem in running GSVA
GSVA getting error in gsva function
9.3 years ago sathyabaarathi • 0
0
votes
9
replies
2.9k
views
problem with using GSVA package
GSVA GSVA
updated 12.5 years ago by ★ 3.3k • written 12.5 years ago by ▴ 360
1
vote
6
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495
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GSVA on separate healthy and disease datasets
GSVA
updated 27 days ago by 65k • written 28 days ago by ▴ 60
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5
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2.5k
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GSVA questions
cdf GSVA cdf GSVA
10.7 years ago Guest User ★ 13k
4
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
4
replies
169
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 2 hours ago by 50k • written 2 days ago by • 0
5
votes
16
replies
2.3k
views
GSVA package scores are opposite on mac and windows
GSVA bug gsva bugs
updated 6.6 years ago by ★ 3.3k • written 6.6 years ago by ▴ 10
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.2 years ago jaison75 ▴ 20
0
votes
11
replies
2.9k
views
GSVA: using Entrez ID's as identifiers
probe GSVA probe GSVA
updated 12.5 years ago by ★ 3.3k • written 12.5 years ago by ▴ 360
0
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5
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2.6k
views
parallel and GSVA
PROcess GSVA PROcess GSVA
updated 11.3 years ago by ★ 13k • written 11.3 years ago by ▴ 130
2
votes
3
replies
1.8k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.4 years ago by ★ 3.3k • written 3.4 years ago by ▴ 20
0
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5
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5.2k
views
Convert gene expression matrix to ExpressionSet
GSVA GSVA
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 360
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3
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2.7k
views
[GSVA] Segfault with GSVA
RNASeq Microarray Annotation gcrma convert GSVA RNASeq Microarray Annotation gcrma GSVA
updated 11.3 years ago by ▴ 230 • written 11.3 years ago by ★ 3.3k
0
votes
5
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2.1k
views
GSVA error
GSVA GSVA
updated 11.3 years ago by ★ 3.3k • written 11.3 years ago by ★ 13k
0
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1
reply
1.4k
views
GSVA
Microarray Pathways GSVA Microarray Pathways GSVA
11.2 years ago Robert Castelo ★ 3.3k
0
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2
replies
1.9k
views
Error when running Gene Set Variant Analysis (GSVA)
GSVA GSVA
updated 10.9 years ago by ★ 3.3k • written 10.9 years ago by ▴ 50
0
votes
1
reply
1.7k
views
nsFilter error in genefilter
GO hgu133plus2 cdf GSVA AnnotationForge GO hgu133plus2 cdf GSVA AnnotationForge
updated 10.8 years ago by 65k • written 10.8 years ago by ▴ 90
2
votes
2
replies
3.5k
views
Error in running gsva function from GSVA package
gsva
updated 8.5 years ago by ★ 3.3k • written 8.5 years ago by ▴ 10
2
votes
1
reply
3.3k
views
Dealing with the output of ssGSEA method from GSVA package
gsva ssgsea
8.5 years ago Momeneh Foroutan ▴ 10
0
votes
3
replies
1.5k
views
GSVA (1.18.0) segfaulting on small dataset
gsva segfault
updated 8.0 years ago by ★ 3.3k • written 8.0 years ago by ▴ 120
3
votes
2
replies
1.4k
views
Crash GSVA 1.24.0 with bootstrapping
GSVA bug
updated 7.0 years ago by ★ 3.3k • written 7.0 years ago by ▴ 20
8
votes
3
replies
2.5k
views
GSVA indifferent to 'abs.ranking'
GSVA gsva abs.ranking
updated 7.0 years ago by ★ 3.3k • written 7.0 years ago by ▴ 130
4
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2
replies
2.6k
views
GSVA: questions about the bootstrap p-value
gsva
updated 6.9 years ago by ★ 3.3k • written 6.9 years ago by ▴ 30
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 5 months ago by ▴ 10 • written 6.8 years ago by ▴ 130
0
votes
1
reply
1.5k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 6.7 years ago by ★ 3.3k • written 6.7 years ago by • 0
2
votes
4
replies
1.4k
views
Failed to install Biobase
GSVA Biobase
updated 13 months ago by 65k • written 13 months ago by • 0
2
votes
7
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1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 8 weeks ago by ▴ 10 • written 2.9 years ago by • 0
0
votes
1
reply
1.2k
views
GSVA package normalization on gene-length ?
GSVA
updated 2.4 years ago by ★ 3.3k • written 2.4 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 2.2 years ago by ★ 3.3k • written 2.2 years ago by • 0
2
votes
2
replies
844
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.9 years ago k.vitting.seerup ▴ 120
0
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1
reply
3.1k
views
GSVA Problem
GSVA
updated 3.0 years ago by ★ 3.3k • written 3.0 years ago by • 0
2
votes
2
replies
1.4k
views
How to run GSVA with partially NA genes
GSVA
23 months ago blakebowen • 0
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
1.1k
views
GSVA results interpretation
GSVA
updated 16 months ago by ★ 3.3k • written 16 months ago by • 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 • 0 • written 14 months ago by • 0
0
votes
3
replies
752
views
GSVA: Error loading interactive web app
igsva GSVA
updated 14 months ago by ★ 3.3k • written 15 months ago by ▴ 40
0
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4
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1.3k
views
The selection of bandwidth of GSVA
GSVA gsva
updated 6.2 years ago by ★ 3.3k • written 6.2 years ago by • 0
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
2
votes
2
replies
1.8k
views
Input genes for GSVA
gsva gene expression matrix
updated 6.1 years ago by ★ 3.3k • written 6.1 years ago by ▴ 70
1
vote
1
reply
1.5k
views
GSVA with NanoString nCounter data
GSVA Nanostring
5.8 years ago • updated 5.1 years ago SB • 0
1
vote
4
replies
2.0k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 5.8 years ago by ★ 3.3k • written 5.8 years ago by • 0
2
votes
1
reply
1.2k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 5.6 years ago by ★ 3.3k • written 5.7 years ago by ▴ 10
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: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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