Showing : DOSE • reset
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
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2
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3.0k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler DOSE
updated 9 months ago by • 0 • written 12 months ago by • 0
0
votes
3
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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 14 months ago by ▴ 10
0
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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
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0
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586
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
2.8 years ago Madza Farias-Virgens • 0
0
votes
2
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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
609
views
Disease semantic similarity
DOSE
4.4 years ago ahmettoprak42 • 0
0
votes
1
reply
829
views
How to change the siez of lables in heatmap
software error go dose heatplot gseGo
4.7 years ago aboumarshal • 0
0
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0
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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
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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
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1.1k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE package installation windows10
6.2 years ago Yisong Zhen ▴ 200
1
vote
3
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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
2.2k
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
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1.5k
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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 9.8 years ago by ▴ 190 • written 9.9 years ago by ★ 12k
0
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0
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1.6k
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question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
9.8 years ago Gordon Smyth 48k
0
votes
0
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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
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3
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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
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0
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954
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR DOSE edgeR DOSE
10.2 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
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1.3k
views
LIMMA: donor effect
Microarray limma DOSE Microarray limma DOSE
updated 12.4 years ago by ▴ 380 • written 12.4 years ago by 48k
0
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0
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1.4k
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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
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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
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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
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9
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4.0k
views
GEOquery installation problem
DOSE DOSE
14.2 years ago zhihua zhang ▴ 50
0
votes
4
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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
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0
replies
1.1k
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Expired Illumina expression chip - advice for use and experimental design
GO limma DOSE GO limma DOSE
15.7 years ago Johnstone, Alice ▴ 410
0
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0
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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
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1
reply
1.3k
views
Re: Limma: M value in toptable
limma DOSE limma DOSE
updated 18.6 years ago by ▴ 60 • written 18.6 years ago by 48k
0
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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
18.6 years ago Dipl.-Ing. Johannes Rainer ▴ 430
0
votes
1
reply
1.9k
views
Dose-Response: Regressiion and ANOVA
Regression DOSE Regression DOSE
updated 18.7 years ago by ▴ 360 • written 18.7 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
954
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: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0
It makes sense that DeSeq2 normalized FPMs are more accurate. Thank you for the information!
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC by James W. MacDonald 63k
If you essentially combined multiple BAM files in the MACS call, you could then just combine them using `samtools cat`, in which case you o…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
I can rephrase your question as: Why is number of reads not the superior estimate for the scaling factor (the "m" in rpm). There are som…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0
Hi Michael, Yes I manually calculated the RPMs by dividing each genes RPM to the library read depth. I didn't do any other normalization …
Comment: shinyMethyl - saving the file by dorota.komar • 0
I tried printing the page as pdf, unfortunately I get the same problem. I guess for now, I will need to save the graphs separately :) Than…
Votes
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Batch correction and Deseq2
A: Read counts between QSEA and MEDIPs
ComBat_seq function in sva package does not return a matrix
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