Showing : dose • reset
2
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3
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813
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
3 months ago • updated 12 weeks ago Yifeii.Ge • 0
1
vote
4
replies
861
views
Error in gseDO function
DOSE gsea
8 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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8.3k
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
5.2k
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 2.6 years ago by ▴ 10
0
votes
0
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1.0k
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.9 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
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943
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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
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2.5k
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 5.2 years ago by 25k • written 5.2 years ago by • 0
0
votes
1
reply
956
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
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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
6.8 years ago alper.kucukural ▴ 10
0
votes
2
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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
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4
replies
3.8k
views
gseDO function input
DOSE clusterprofiler
updated 7.5 years ago by ★ 1.2k • written 7.5 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
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1.9k
views
Subset of genes can find a term but whole set cannot
biomart dose
updated 7.7 years ago by 67k • written 7.7 years ago by • 0
2
votes
5
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2.1k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 8.0 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 8.3 years ago by 25k • written 8.3 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
9.2 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
10.5 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
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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
11.6 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 11.6 years ago by ★ 8.2k • written 11.6 years ago by ★ 13k
0
votes
0
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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
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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
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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
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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 14.2 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 14.2 years ago by ★ 4.3k • written 14.2 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 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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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
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Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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