Showing : DOSE • reset
2
votes
3
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786
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
11 weeks ago Yifeii.Ge • 0
1
vote
4
replies
841
views
Error in gseDO function
DOSE gsea
7 months ago Javier • 0
0
votes
1
reply
1.4k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
4
votes
4
replies
5.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.3 years ago by • 0 • written 8.4 years ago by ▴ 660
1
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2
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8.2k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler DOSE
updated 2.1 years ago by • 0 • written 2.4 years ago by • 0
0
votes
3
replies
5.1k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler enrichplot clusterpro doseR dose
updated 2.5 years ago by ★ 4.1k • written 2.5 years ago by ▴ 10
0
votes
0
replies
1.0k
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.9 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
939
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.2 years ago Madza Farias-Virgens • 0
0
votes
2
replies
2.4k
views
DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
software error reactomePA DOSE DO.db there is no package called ‘DO.db’
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
0
votes
1
reply
947
views
Disease semantic similarity
DOSE
5.7 years ago ahmettoprak42 • 0
0
votes
1
reply
1.2k
views
How to change the siez of lables in heatmap
software error go dose heatplot gseGo
6.0 years ago aboumarshal • 0
0
votes
0
replies
1.8k
views
Moving around nodes using emapplot {enrichplot} or enrichMap {DOSE}
enrichment map emapplot enrichplot enrichMap DOSE
6.6 years ago jan.soderman • 0
1
vote
1
reply
1.5k
views
dotplot in DOSE
compilation error DOSE
6.7 years ago alper.kucukural ▴ 10
0
votes
2
replies
1.9k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by • 0
2
votes
2
replies
4.1k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by ▴ 20
1
vote
4
replies
3.8k
views
gseDO function input
DOSE clusterprofiler
updated 7.4 years ago by ★ 1.2k • written 7.4 years ago by • 0
0
votes
3
replies
1.6k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE package installation windows10
7.6 years ago Yisong Zhen ▴ 200
1
vote
3
replies
1.9k
views
Subset of genes can find a term but whole set cannot
biomart dose
updated 7.6 years ago by 67k • written 7.6 years ago by • 0
2
votes
5
replies
2.1k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 7.9 years ago by 43k • written 8.0 years ago by • 0
1
vote
1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
8.0 years ago Kajus Baidžajevas ▴ 10
4
votes
3
replies
2.4k
views
BiocParallel: object export issue
BiocParallel DOSE
updated 8.2 years ago by 25k • written 8.2 years ago by ★ 4.1k
2
votes
6
replies
3.8k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler DOSE GSEA_internal USER_DATA leading edge Analysis
8.3 years ago Riba Michela ▴ 90
0
votes
0
replies
3.1k
views
Modifying the legend in cnetplot function
clusterProfiler DOSE
9.1 years ago Vinicius Henrique da Silva ▴ 40
1
vote
1
reply
1.8k
views
Treatment dose in treatment-control RNA-seq
deseq2 edger dose rna-seq
updated 9.2 years ago by ★ 28k • written 9.2 years ago by • 0
0
votes
0
replies
1.9k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
10.2 years ago Guangchuang Yu ★ 1.2k
0
votes
1
reply
1.6k
views
strange log2FoldChange estimates
RNASeq DOSE DESeq2 RNASeq DOSE DESeq2
10.4 years ago Shi, Tao ▴ 720
0
votes
2
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2.0k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray DOSE Microarray DOSE
updated 11.2 years ago by ▴ 190 • written 11.2 years ago by ★ 13k
0
votes
0
replies
1.9k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
11.2 years ago Gordon Smyth 52k
0
votes
0
replies
1.6k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO Cancer Rgraphviz clusterProfiler DOSE GO Cancer Rgraphviz clusterProfiler DOSE
11.5 years ago Martin Morgan 25k
0
votes
3
replies
2.1k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO clusterProfiler DOSE GO clusterProfiler DOSE
updated 11.5 years ago by ★ 8.2k • written 11.5 years ago by ★ 13k
0
votes
0
replies
1.3k
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR DOSE edgeR DOSE
11.6 years ago Sandhya Pemmasani Kiran ▴ 40
0
votes
1
reply
2.3k
views
Question on unbalanced paired design
Microarray Normalization GO limma DOSE Microarray Normalization GO limma DOSE
updated 11.8 years ago by ★ 7.9k • written 11.8 years ago by ▴ 40
0
votes
2
replies
1.5k
views
about limma linear models
Microarray limma DOSE Microarray limma DOSE
updated 13.7 years ago by ▴ 40 • written 13.7 years ago by 52k
0
votes
1
reply
1.8k
views
LIMMA: donor effect
Microarray limma DOSE Microarray limma DOSE
updated 13.8 years ago by ▴ 380 • written 13.8 years ago by 52k
0
votes
0
replies
1.6k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
14.1 years ago Roman ▴ 20
0
votes
2
replies
1.8k
views
FW: PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 14.1 years ago by ▴ 120 • written 14.1 years ago by ▴ 10
0
votes
2
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2.0k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 14.1 years ago by ★ 4.3k • written 14.1 years ago by ▴ 120
1
vote
2
replies
2.7k
views
Regression using LIMMA
affy limma DOSE affy limma DOSE
updated 14.2 years ago by ★ 6.0k • written 14.2 years ago by ▴ 380
0
votes
1
reply
1.5k
views
limma: writing down the matrix in an almost (?) factorial design experiment
Microarray DOSE Microarray DOSE
15.0 years ago • updated 14.9 years ago Massimo Pinto ▴ 390
0
votes
9
replies
5.1k
views
GEOquery installation problem
DOSE DOSE
15.5 years ago zhihua zhang ▴ 50
0
votes
4
replies
1.8k
views
GEO annotation
Annotation DOSE Annotation DOSE
updated 16.6 years ago by ★ 7.2k • written 16.6 years ago by ▴ 110
0
votes
5
replies
3.3k
views
Finding genes with significant linear regression or trend
Microarray Regression Cancer limma DOSE Microarray Regression Cancer limma DOSE
updated 16.7 years ago by ▴ 340 • written 16.7 years ago by ★ 1.9k
0
votes
0
replies
1.3k
views
Expired Illumina expression chip - advice for use and experimental design
GO limma DOSE GO limma DOSE
17.0 years ago Johnstone, Alice ▴ 410
0
votes
0
replies
1.3k
views
about microarray batch effect and treatment effect
affy DOSE affy DOSE
17.1 years ago Aedin Culhane ▴ 510
0
votes
0
replies
1.3k
views
microarray analysis of a dose response * strain experiment
Microarray affy limma maSigPro DOSE BRAIN Microarray affy limma maSigPro DOSE BRAIN
18.2 years ago Naomi Altman ★ 6.0k
0
votes
4
replies
1.8k
views
microarray analysis of a dose response * strain experiment
affy DOSE BRAIN affy DOSE BRAIN
updated 18.2 years ago by 21k • written 18.2 years ago by ▴ 890
0
votes
1
reply
1.7k
views
Re: Limma: M value in toptable
limma DOSE limma DOSE
updated 20.0 years ago by ▴ 60 • written 20.0 years ago by 52k
0
votes
0
replies
1.8k
views
RMA normalization,which samples should be normalized together
Normalization probe affy limma gcrma DOSE Normalization probe affy limma gcrma DOSE
20.0 years ago Dipl.-Ing. Johannes Rainer ▴ 430
0
votes
1
reply
2.3k
views
Dose-Response: Regressiion and ANOVA
Regression DOSE Regression DOSE
updated 20.1 years ago by ▴ 360 • written 20.1 years ago by ▴ 620
0
votes
1
reply
1.3k
views
normalizaton between studies
Normalization vsn DOSE Normalization vsn DOSE
updated 20.1 years ago by ▴ 10 • written 20.1 years ago by ▴ 620
50 results • Page 1 of 1
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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
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?
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