Showing : GSVA • reset
6
votes
4
replies
203
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3 months ago • updated 12 weeks ago hanyin.wang88 ▴ 10
0
votes
4
replies
196
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
3 months ago • updated 12 weeks ago Siyuan • 0
0
votes
3
replies
227
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4 months ago by ★ 2.7k • written 4 months ago by • 0
0
votes
3
replies
190
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 6 months ago by ★ 2.7k • written 6 months ago by ▴ 60
0
votes
10
replies
545
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 8 weeks ago by 2.9k • written 8 months ago by • 0
0
votes
1
reply
118
views
Extract GSVA gene rank matrix
gsva
updated 9 months ago by ★ 2.7k • written 9 months ago by • 0
2
votes
1
reply
222
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 10 months ago by ★ 2.7k • written 10 months ago by ▴ 40
2
votes
2
replies
160
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 10 months ago by ★ 2.7k • written 10 months ago by • 0
0
votes
10
replies
418
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 10 months ago by ★ 2.7k • written 10 months ago by • 0
0
votes
1
reply
169
views
GSVA on integrated/batch corrected scRNAseq data
GSVA Job
updated 11 months ago by ★ 2.7k • written 11 months ago by • 0
1
vote
12
replies
414
views
GSVA (running group samples separately)
GSVA
updated 12 months ago by ★ 2.7k • written 12 months ago by ▴ 30
7
votes
11
replies
390
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 12 months ago by ★ 2.7k • written 12 months ago by ▴ 60
0
votes
1
reply
136
views
Method and kcdf arguments in gsva package
GSVA
updated 12 months ago by ★ 2.7k • written 12 months ago by ▴ 10
4
votes
6
replies
13k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 7 weeks ago by • 0 • written 3.8 years ago by ▴ 90
1
vote
4
replies
1.1k
views
GSVA on RNAseq data
gsva rnaseq
updated 2.1 years ago by ★ 2.7k • written 2.1 years ago by ▴ 60
0
votes
1
reply
263
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 2.1 years ago by ★ 2.7k • written 2.1 years ago by • 0
1
vote
1
reply
546
views
GSVA with NanoString nCounter data
GSVA Nanostring
2.8 years ago • updated 2.1 years ago SB • 0
5
votes
4
replies
630
views
Differential expression on GSVA scores using LIMMA
limma gsva
updated 2.1 years ago by ★ 2.7k • written 2.1 years ago by ▴ 60
2
votes
4
replies
555
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4 months ago by • 0 • written 2.2 years ago by ▴ 30
10
votes
10
replies
1.8k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
3.1 years ago • updated 2.3 years ago rached ▴ 50
0
votes
0
replies
400
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
2.3 years ago Pietro ▴ 30
1
vote
1
reply
350
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
2.3 years ago krassowski.michal ▴ 10
2
votes
1
reply
414
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 2.6 years ago by ★ 2.7k • written 2.7 years ago by • 0
1
vote
4
replies
594
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 2.8 years ago by ★ 2.7k • written 2.8 years ago by • 0
1
vote
2
replies
501
views
Input genes for GSVA
gsva gene expression matrix
updated 3.1 years ago by ★ 2.7k • written 3.1 years ago by ▴ 60
0
votes
4
replies
425
views
The selection of bandwidth of GSVA
GSVA gsva
updated 3.2 years ago by ★ 2.7k • written 3.2 years ago by • 0
1
vote
2
replies
703
views
GSVA for single sample
gsea gsva ssgsea
3.3 years ago jaison75 ▴ 20
5
votes
16
replies
861
views
GSVA package scores are opposite on mac and windows
GSVA bug gsva bugs
updated 3.6 years ago by ★ 2.7k • written 3.6 years ago by ▴ 10
0
votes
1
reply
765
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 3.7 years ago by ★ 2.7k • written 3.8 years ago by • 0
3
votes
2
replies
1.1k
views
GSVA: questions about the bootstrap p-value
gsva
updated 3.9 years ago by ★ 2.7k • written 3.9 years ago by ▴ 20
2
votes
9
replies
4.2k
views
Does GSVA enrichment score comes negative?
GSVA
4.9 years ago • updated 4.0 years ago pbachali ▴ 20
8
votes
3
replies
1.2k
views
GSVA indifferent to 'abs.ranking'
GSVA gsva abs.ranking
updated 4.0 years ago by ★ 2.7k • written 4.0 years ago by ▴ 90
3
votes
2
replies
683
views
Crash GSVA 1.24.0 with bootstrapping
GSVA bug
updated 4.0 years ago by ★ 2.7k • written 4.0 years ago by ▴ 20
0
votes
1
reply
726
views
GSVA es.obs why range is between -1 and 1
gsva
4.7 years ago Adrian Johnson ▴ 330
1
vote
0
replies
852
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
4.7 years ago t.kuilman 170
1
vote
2
replies
564
views
Method to be used in gsva() function
GSVA
4.8 years ago pbachali ▴ 20
0
votes
3
replies
692
views
GSVA (1.18.0) segfaulting on small dataset
gsva segfault
updated 5.0 years ago by ★ 2.7k • written 5.0 years ago by ▴ 120
2
votes
5
replies
1.2k
views
GSVA error - incomplete instalation?
GSVA ExpressionSet
5.5 years ago • updated 5.4 years ago thrabe • 0
2
votes
1
reply
2.2k
views
Dealing with the output of ssGSEA method from GSVA package
gsva ssgsea
5.5 years ago Momeneh Foroutan ▴ 10
2
votes
2
replies
1.5k
views
Error in running gsva function from GSVA package
gsva
updated 5.5 years ago by ★ 2.7k • written 5.5 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Problem in running GSVA
GSVA getting error in gsva function
6.3 years ago sathyabaarathi • 0
0
votes
8
replies
2.1k
views
GSVA: problem with chip annotation
gsva
updated 6.5 years ago by ★ 2.7k • written 6.5 years ago by • 0
2
votes
5
replies
1.6k
views
Problem encountered when running GSVA for RNAseq
gsva rnaseq
updated 6.5 years ago by ★ 2.7k • written 6.5 years ago by • 0
0
votes
0
replies
777
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
7.5 years ago Gordon Smyth 42k
0
votes
0
replies
654
views
enrichment packages that accept t-stat (or related stat) as input
Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category
7.6 years ago Pekka Kohonen ▴ 190
0
votes
5
replies
1.4k
views
GSVA questions
cdf GSVA cdf GSVA
7.7 years ago Guest User ★ 12k
0
votes
3
replies
773
views
about running gsva on mac
PROcess GSVA PROcess GSVA
updated 7.8 years ago by ▴ 200 • written 7.8 years ago by ▴ 230
0
votes
1
reply
1.0k
views
nsFilter error in genefilter
GO hgu133plus2 cdf GSVA AnnotationForge GO hgu133plus2 cdf GSVA AnnotationForge
updated 7.8 years ago by 56k • written 7.9 years ago by ▴ 90
0
votes
2
replies
1.0k
views
Error when running Gene Set Variant Analysis (GSVA)
GSVA GSVA
updated 7.9 years ago by ★ 2.7k • written 7.9 years ago by ▴ 50
0
votes
5
replies
2.1k
views
nsFilter error in genefilter
GSVA GSVA
updated 8.1 years ago by ★ 2.7k • written 8.1 years ago by ★ 12k
50 results • Page 1 of 1
Recent ...
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Answer: DiffBind by Rory Stark ★ 3.8k
I'll answer the second question first. You should not accessing the `$binding` matrix directly -- the chromosome names are factor numbers,…
Comment: How to download the ChAMP dependency ChAMPdata by shepherl 2.6k
You could try increasing the timeout limit for downloading files. I increased mine in a `.Rprofile` script so its persistent in all sessio…
Comment: DiffBind reporting error by Rory Stark ★ 3.8k
If you could give me access to your `dbind_de` object, I can have a look at what is going on. it would help to see the sequence of calls yo…
Comment: limma - removing samples? by RMP87 • 0
Thank you very much for the explanation. Making it more precise. Could I analyze and normalize all samples from a dataset even though I had…
Comment: DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ? by Saulius • 0
Yes - I think you are right once more. Thanks for taking so much time to look into this. Size factors come in twice in the code of `cqn`: …
Votes
What does dba.PCA in DiffBind exactly do?
Answer: How to retrieve peak summit from DiffBind peaks
Comment: How to download the ChAMP dependency ChAMPdata
Effect of feature number on adjusted p-values
Effect of feature number on adjusted p-values
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