Showing : DOSE • reset
2
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3
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494
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
8 days ago • updated 7 days ago Yifeii.Ge • 0
1
vote
4
replies
654
views
Error in gseDO function
DOSE gsea
5 months ago Javier • 0
0
votes
1
reply
1.0k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 6 months ago by ★ 4.1k • written 7 months ago by • 0
4
votes
4
replies
4.9k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.1 years ago by • 0 • written 8.2 years ago by ▴ 660
1
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2
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7.6k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler DOSE
updated 22 months ago by • 0 • written 2.2 years ago by • 0
0
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3
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4.7k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler enrichplot clusterpro doseR dose
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by ▴ 10
0
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0
replies
969
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.7 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
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888
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
3.9 years ago Madza Farias-Virgens • 0
0
votes
2
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2.3k
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 4.9 years ago by 25k • written 4.9 years ago by • 0
0
votes
1
reply
912
views
Disease semantic similarity
DOSE
5.5 years ago ahmettoprak42 • 0
0
votes
1
reply
1.1k
views
How to change the siez of lables in heatmap
software error go dose heatplot gseGo
5.8 years ago aboumarshal • 0
0
votes
0
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1.7k
views
Moving around nodes using emapplot {enrichplot} or enrichMap {DOSE}
enrichment map emapplot enrichplot enrichMap DOSE
6.4 years ago jan.soderman • 0
1
vote
1
reply
1.4k
views
dotplot in DOSE
compilation error DOSE
6.5 years ago alper.kucukural ▴ 10
0
votes
2
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1.8k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
2
votes
2
replies
3.9k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by ▴ 20
1
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4
replies
3.6k
views
gseDO function input
DOSE clusterprofiler
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by • 0
0
votes
3
replies
1.5k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE package installation windows10
7.4 years ago • updated 7.3 years ago Yisong Zhen ▴ 200
1
vote
3
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1.8k
views
Subset of genes can find a term but whole set cannot
biomart dose
updated 7.4 years ago by 67k • written 7.4 years ago by • 0
2
votes
5
replies
2.0k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 7.7 years ago by 42k • written 7.7 years ago by • 0
1
vote
1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.8 years ago Kajus Baidžajevas ▴ 10
4
votes
3
replies
2.2k
views
BiocParallel: object export issue
BiocParallel DOSE
updated 8.0 years ago by 25k • written 8.0 years ago by ★ 4.1k
2
votes
6
replies
3.6k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler DOSE GSEA_internal USER_DATA leading edge Analysis
8.1 years ago Riba Michela ▴ 90
0
votes
0
replies
3.0k
views
Modifying the legend in cnetplot function
clusterProfiler DOSE
8.9 years ago Vinicius Henrique da Silva ▴ 40
1
vote
1
reply
1.7k
views
Treatment dose in treatment-control RNA-seq
deseq2 edger dose rna-seq
updated 9.0 years ago by ★ 28k • written 9.0 years ago by • 0
0
votes
0
replies
1.8k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
10.0 years ago Guangchuang Yu ★ 1.2k
0
votes
1
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1.5k
views
strange log2FoldChange estimates
RNASeq DOSE DESeq2 RNASeq DOSE DESeq2
10.2 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 11.0 years ago by ▴ 190 • written 11.0 years ago by ★ 13k
0
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0
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1.8k
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question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
11.0 years ago Gordon Smyth 51k
0
votes
0
replies
1.5k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO Cancer Rgraphviz clusterProfiler DOSE GO Cancer Rgraphviz clusterProfiler DOSE
11.3 years ago Martin Morgan 25k
0
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3
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2.0k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO clusterProfiler DOSE GO clusterProfiler DOSE
updated 11.3 years ago by ★ 8.2k • written 11.3 years ago by ★ 13k
0
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0
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1.2k
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR DOSE edgeR DOSE
11.4 years ago Sandhya Pemmasani Kiran ▴ 40
0
votes
1
reply
2.2k
views
Question on unbalanced paired design
Microarray Normalization GO limma DOSE Microarray Normalization GO limma DOSE
updated 11.6 years ago by ★ 7.9k • written 11.6 years ago by ▴ 40
0
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2
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1.5k
views
about limma linear models
Microarray limma DOSE Microarray limma DOSE
updated 13.5 years ago by ▴ 40 • written 13.5 years ago by 51k
0
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1
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1.7k
views
LIMMA: donor effect
Microarray limma DOSE Microarray limma DOSE
updated 13.5 years ago by ▴ 380 • written 13.5 years ago by 51k
0
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0
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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
13.9 years ago Roman ▴ 20
0
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2
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1.7k
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 13.9 years ago by ▴ 120 • written 13.9 years ago by ▴ 10
0
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2
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1.9k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 13.9 years ago by ★ 4.3k • written 13.9 years ago by ▴ 120
1
vote
2
replies
2.6k
views
Regression using LIMMA
affy limma DOSE affy limma DOSE
updated 14.0 years ago by ★ 6.0k • written 14.0 years ago by ▴ 380
0
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1
reply
1.4k
views
limma: writing down the matrix in an almost (?) factorial design experiment
Microarray DOSE Microarray DOSE
14.7 years ago Massimo Pinto ▴ 390
0
votes
9
replies
4.9k
views
GEOquery installation problem
DOSE DOSE
15.3 years ago zhihua zhang ▴ 50
0
votes
4
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1.7k
views
GEO annotation
Annotation DOSE Annotation DOSE
updated 16.4 years ago by ★ 7.2k • written 16.4 years ago by ▴ 110
0
votes
5
replies
3.2k
views
Finding genes with significant linear regression or trend
Microarray Regression Cancer limma DOSE Microarray Regression Cancer limma DOSE
updated 16.5 years ago by ▴ 340 • written 16.5 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
16.8 years ago Johnstone, Alice ▴ 410
0
votes
0
replies
1.2k
views
about microarray batch effect and treatment effect
affy DOSE affy DOSE
16.9 years ago Aedin Culhane ▴ 510
0
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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
18.0 years ago Naomi Altman ★ 6.0k
0
votes
4
replies
1.7k
views
microarray analysis of a dose response * strain experiment
affy DOSE BRAIN affy DOSE BRAIN
updated 18.0 years ago by 21k • written 18.0 years ago by ▴ 890
0
votes
1
reply
1.6k
views
Re: Limma: M value in toptable
limma DOSE limma DOSE
updated 19.7 years ago by ▴ 60 • written 19.8 years ago by 51k
0
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0
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1.8k
views
RMA normalization,which samples should be normalized together
Normalization probe affy limma gcrma DOSE Normalization probe affy limma gcrma DOSE
19.8 years ago Dipl.-Ing. Johannes Rainer ▴ 430
0
votes
1
reply
2.3k
views
Dose-Response: Regressiion and ANOVA
Regression DOSE Regression DOSE
updated 19.8 years ago by ▴ 360 • written 19.8 years ago by ▴ 620
0
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1
reply
1.3k
views
normalizaton between studies
Normalization vsn DOSE Normalization vsn DOSE
updated 19.9 years ago by ▴ 10 • written 19.9 years ago by ▴ 620
50 results • Page 1 of 1
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Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Fahd • 0
Thanks for looking into this. This issue results in the incorrect usage of multiple ORA software including EnrichR.
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
Yes, I understand the implications of replacing the `OrgDb` packages in release. Maybe an upload to the annotationHub or GitHub could be an…
Votes
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
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