Showing : dose • reset
4
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4
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3.3k
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Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 11 months ago by • 0 • written 7.1 years ago by ▴ 660
1
vote
2
replies
3.0k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler DOSE
updated 9 months ago by • 0 • written 13 months ago by • 0
0
votes
3
replies
2.1k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler enrichplot clusterpro doseR dose
updated 14 months ago by ★ 3.7k • written 15 months ago by ▴ 10
0
votes
0
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640
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
2.6 years ago Lluís Revilla Sancho ▴ 720
0
votes
0
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590
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
2.9 years ago Madza Farias-Virgens • 0
0
votes
2
replies
1.7k
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 3.8 years ago by 25k • written 3.8 years ago by • 0
0
votes
1
reply
614
views
Disease semantic similarity
DOSE
4.4 years ago ahmettoprak42 • 0
0
votes
1
reply
833
views
How to change the siez of lables in heatmap
software error go dose heatplot gseGo
4.7 years ago aboumarshal • 0
0
votes
0
replies
1.2k
views
Moving around nodes using emapplot {enrichplot} or enrichMap {DOSE}
enrichment map emapplot enrichplot enrichMap DOSE
5.3 years ago jan.soderman • 0
1
vote
1
reply
994
views
dotplot in DOSE
compilation error DOSE
5.4 years ago alper.kucukural ▴ 10
0
votes
2
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1.3k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 5.7 years ago by ★ 1.2k • written 5.7 years ago by • 0
2
votes
2
replies
3.0k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by • 0
1
vote
4
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2.6k
views
gseDO function input
DOSE clusterprofiler
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
0
votes
3
replies
1.1k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE package installation windows10
6.3 years ago • updated 6.2 years ago Yisong Zhen ▴ 200
1
vote
3
replies
1.4k
views
Subset of genes can find a term but whole set cannot
biomart dose
updated 6.3 years ago by 63k • written 6.3 years ago by • 0
2
votes
5
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1.6k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 6.6 years ago by 40k • written 6.6 years ago by • 0
1
vote
1
reply
1.4k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
6.7 years ago Kajus Baidžajevas ▴ 10
4
votes
3
replies
1.6k
views
BiocParallel: object export issue
BiocParallel DOSE
updated 6.9 years ago by 25k • written 6.9 years ago by ★ 3.7k
2
votes
6
replies
2.7k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler DOSE GSEA_internal USER_DATA leading edge Analysis
7.0 years ago Riba Michela ▴ 90
0
votes
0
replies
2.3k
views
Modifying the legend in cnetplot function
clusterProfiler DOSE
7.8 years ago Vinicius Henrique da Silva ▴ 40
1
vote
1
reply
1.4k
views
Treatment dose in treatment-control RNA-seq
deseq2 edger dose rna-seq
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
0
replies
1.5k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
8.9 years ago Guangchuang Yu ★ 1.2k
0
votes
1
reply
1.2k
views
strange log2FoldChange estimates
RNASeq DOSE DESeq2 RNASeq DOSE DESeq2
9.1 years ago Shi, Tao ▴ 720
0
votes
2
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1.6k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray DOSE Microarray DOSE
updated 9.9 years ago by ▴ 190 • written 9.9 years ago by ★ 12k
0
votes
0
replies
1.6k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
9.9 years ago Gordon Smyth 48k
0
votes
0
replies
1.2k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO Cancer Rgraphviz clusterProfiler DOSE GO Cancer Rgraphviz clusterProfiler DOSE
10.2 years ago Martin Morgan 25k
0
votes
3
replies
1.6k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO clusterProfiler DOSE GO clusterProfiler DOSE
updated 10.2 years ago by ★ 8.2k • written 10.2 years ago by ★ 12k
0
votes
0
replies
956
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR DOSE edgeR DOSE
10.3 years ago Sandhya Pemmasani Kiran ▴ 40
0
votes
1
reply
2.0k
views
Question on unbalanced paired design
Microarray Normalization GO limma DOSE Microarray Normalization GO limma DOSE
updated 10.5 years ago by 7.8k • written 10.5 years ago by ▴ 40
0
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2
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1.1k
views
about limma linear models
Microarray limma DOSE Microarray limma DOSE
updated 12.4 years ago by ▴ 40 • written 12.4 years ago by 48k
0
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1
reply
1.3k
views
LIMMA: donor effect
Microarray limma DOSE Microarray limma DOSE
updated 12.5 years ago by ▴ 380 • written 12.5 years ago by 48k
0
votes
0
replies
1.4k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
12.8 years ago Roman ▴ 20
0
votes
2
replies
1.4k
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 12.8 years ago by ▴ 120 • written 12.8 years ago by ▴ 10
0
votes
2
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
updated 12.8 years ago by ★ 4.3k • written 12.8 years ago by ▴ 120
1
vote
2
replies
2.3k
views
Regression using LIMMA
affy limma DOSE affy limma DOSE
updated 12.9 years ago by ★ 6.0k • written 12.9 years ago by ▴ 380
0
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1
reply
1.1k
views
limma: writing down the matrix in an almost (?) factorial design experiment
Microarray DOSE Microarray DOSE
13.6 years ago Massimo Pinto ▴ 390
0
votes
9
replies
4.0k
views
GEOquery installation problem
DOSE DOSE
14.2 years ago zhihua zhang ▴ 50
0
votes
4
replies
1.4k
views
GEO annotation
Annotation DOSE Annotation DOSE
updated 15.3 years ago by ★ 7.2k • written 15.3 years ago by ▴ 110
0
votes
5
replies
2.8k
views
Finding genes with significant linear regression or trend
Microarray Regression Cancer limma DOSE Microarray Regression Cancer limma DOSE
updated 15.4 years ago by ▴ 340 • written 15.4 years ago by ★ 1.9k
0
votes
0
replies
1.1k
views
Expired Illumina expression chip - advice for use and experimental design
GO limma DOSE GO limma DOSE
15.7 years ago Johnstone, Alice ▴ 410
0
votes
0
replies
1.0k
views
about microarray batch effect and treatment effect
affy DOSE affy DOSE
15.8 years ago Aedin Culhane ▴ 510
0
votes
0
replies
1.0k
views
microarray analysis of a dose response * strain experiment
Microarray affy limma maSigPro DOSE BRAIN Microarray affy limma maSigPro DOSE BRAIN
16.9 years ago Naomi Altman ★ 6.0k
0
votes
4
replies
1.2k
views
microarray analysis of a dose response * strain experiment
affy DOSE BRAIN affy DOSE BRAIN
updated 16.9 years ago by 21k • written 16.9 years ago by ▴ 890
0
votes
1
reply
1.3k
views
Re: Limma: M value in toptable
limma DOSE limma DOSE
updated 18.7 years ago by ▴ 60 • written 18.7 years ago by 48k
0
votes
0
replies
1.4k
views
RMA normalization,which samples should be normalized together
Normalization probe affy limma gcrma DOSE Normalization probe affy limma gcrma DOSE
18.7 years ago Dipl.-Ing. Johannes Rainer ▴ 430
0
votes
1
reply
1.9k
views
Dose-Response: Regressiion and ANOVA
Regression DOSE Regression DOSE
updated 18.8 years ago by ▴ 360 • written 18.8 years ago by ▴ 620
0
votes
1
reply
1.0k
views
normalizaton between studies
Normalization vsn DOSE Normalization vsn DOSE
updated 18.8 years ago by ▴ 10 • written 18.8 years ago by ▴ 620
0
votes
1
reply
1.1k
views
unbalanced design
limma DOSE limma DOSE
updated 18.8 years ago by 48k • written 18.8 years ago by ▴ 620
0
votes
0
replies
957
views
Friedman test
DOSE DOSE
19.1 years ago Arne.Muller@aventis.com ▴ 620
0
votes
0
replies
1.3k
views
Anova with ratios
affy DOSE affy DOSE
19.3 years ago Arne.Muller@aventis.com ▴ 620
50 results • Page 1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results by James W. MacDonald 63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences by Hervé Pagès 16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results by camillab. ▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
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