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dose
•
reset
1
vote
2
replies
5.1k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler
DOSE
updated 15 months ago by
Nick O
• 0 • written 18 months ago by
ummscr
• 0
0
votes
9
replies
4.4k
views
GEOquery installation problem
DOSE
DOSE
14.7 years ago
zhihua zhang
▴ 50
4
votes
4
replies
4.1k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 17 months ago by
12133067
• 0 • written 7.6 years ago by
enricoferrero
▴ 660
0
votes
3
replies
3.4k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler
enrichplot
clusterpro
doseR
dose
updated 20 months ago by
Guido Hooiveld
★ 3.9k • written 21 months ago by
rama
▴ 10
2
votes
2
replies
3.4k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE
clusterprofiler
annotation
gene ontology
gene set enrichment
updated 6.4 years ago by
Guangchuang Yu
★ 1.2k • written 6.4 years ago by
kirannbishwa01
• 0
2
votes
6
replies
3.0k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler
DOSE
GSEA_internal
USER_DATA
leading edge Analysis
7.5 years ago
Riba Michela
▴ 90
1
vote
4
replies
3.0k
views
gseDO function input
DOSE
clusterprofiler
updated 6.6 years ago by
Guangchuang Yu
★ 1.2k • written 6.6 years ago by
xr2120
• 0
0
votes
5
replies
3.0k
views
Finding genes with significant linear regression or trend
Microarray
Regression
Cancer
limma
DOSE
Microarray
Regression
Cancer
limma
DOSE
updated 15.9 years ago by
Ana Conesa
▴ 340 • written 15.9 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
2.6k
views
Modifying the legend in cnetplot function
clusterProfiler
DOSE
8.3 years ago
Vinicius Henrique da Silva
▴ 40
1
vote
2
replies
2.4k
views
Regression using LIMMA
affy
limma
DOSE
affy
limma
DOSE
updated 13.4 years ago by
Naomi Altman
★ 6.0k • written 13.4 years ago by
fire1976 wyoming
▴ 380
0
votes
1
reply
2.1k
views
Question on unbalanced paired design
Microarray
Normalization
GO
limma
DOSE
Microarray
Normalization
GO
limma
DOSE
updated 11.0 years ago by
Ryan C. Thompson
★ 7.9k • written 11.0 years ago by
Sandhya Pemmasani Kiran
▴ 40
0
votes
1
reply
2.1k
views
Dose-Response: Regressiion and ANOVA
Regression
DOSE
Regression
DOSE
updated 19.2 years ago by
Liaw, Andy
▴ 360 • written 19.2 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
2
replies
2.0k
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 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
goodwinjinesh
• 0
4
votes
3
replies
1.8k
views
BiocParallel: object export issue
BiocParallel
DOSE
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
3
replies
1.8k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO
clusterProfiler
DOSE
GO
clusterProfiler
DOSE
updated 10.7 years ago by
Dan Tenenbaum
★ 8.2k • written 10.7 years ago by
Guest User
★ 13k
0
votes
2
replies
1.8k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray
DOSE
Microarray
DOSE
updated 10.3 years ago by
Pekka Kohonen
▴ 190 • written 10.4 years ago by
Guest User
★ 13k
2
votes
5
replies
1.7k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2
multiple time points
dose
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
stwestreich
• 0
0
votes
2
replies
1.7k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation
cdf
probe
affy
oligo
xps
DOSE
Annotation
cdf
probe
affy
oligo
xps
DOSE
updated 13.3 years ago by
Benilton Carvalho
★ 4.3k • written 13.3 years ago by
branislav misovic
▴ 120
0
votes
0
replies
1.7k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray
limma
DOSE
Microarray
limma
DOSE
10.3 years ago
Gordon Smyth
50k
0
votes
0
replies
1.6k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
9.4 years ago
Guangchuang Yu
★ 1.2k
1
vote
3
replies
1.6k
views
Subset of genes can find a term but whole set cannot
biomart
dose
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
ankita.mandal28529
• 0
0
votes
4
replies
1.5k
views
GEO annotation
Annotation
DOSE
Annotation
DOSE
updated 15.8 years ago by
Marc Carlson
★ 7.2k • written 15.8 years ago by
Roumyana Yordanova
▴ 110
1
vote
1
reply
1.5k
views
ReactomePA viewPathway DE node and legend colour
DOSE
ReactomePA
7.2 years ago
Kajus Baidžajevas
▴ 10
0
votes
0
replies
1.5k
views
RMA normalization,which samples should be normalized together
Normalization
probe
affy
limma
gcrma
DOSE
Normalization
probe
affy
limma
gcrma
DOSE
19.1 years ago
Dipl.-Ing. Johannes Rainer
▴ 430
1
vote
1
reply
1.5k
views
Treatment dose in treatment-control RNA-seq
deseq2
edger
dose
rna-seq
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
JacobK
• 0
0
votes
2
replies
1.5k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE
ReactomePA
enrichMap
enrichPathway
updated 6.2 years ago by
Guangchuang Yu
★ 1.2k • written 6.2 years ago by
jan.soderman
• 0
0
votes
2
replies
1.5k
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 13.3 years ago by
branislav misovic
▴ 120 • written 13.3 years ago by
Ramil Nurtdinov
▴ 10
0
votes
1
reply
1.5k
views
LIMMA: donor effect
Microarray
limma
DOSE
Microarray
limma
DOSE
updated 12.9 years ago by
fire1976 wyoming
▴ 380 • written 12.9 years ago by
Gordon Smyth
50k
0
votes
0
replies
1.5k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation
cdf
probe
affy
oligo
xps
DOSE
Annotation
cdf
probe
affy
oligo
xps
DOSE
13.3 years ago
Roman
▴ 20
0
votes
1
reply
1.5k
views
Re: Limma: M value in toptable
limma
DOSE
limma
DOSE
updated 19.1 years ago by
Hua Weng
▴ 60 • written 19.1 years ago by
Gordon Smyth
50k
0
votes
0
replies
1.4k
views
Moving around nodes using emapplot {enrichplot} or enrichMap {DOSE}
enrichment map
emapplot
enrichplot
enrichMap
DOSE
5.8 years ago
jan.soderman
• 0
0
votes
0
replies
1.4k
views
Anova with ratios
affy
DOSE
affy
DOSE
19.8 years ago
Arne.Muller@aventis.com
▴ 620
0
votes
4
replies
1.4k
views
microarray analysis of a dose response * strain experiment
affy
DOSE
BRAIN
affy
DOSE
BRAIN
updated 17.4 years ago by
Sean Davis
21k • written 17.4 years ago by
Kimpel, Mark W
▴ 890
0
votes
1
reply
1.3k
views
strange log2FoldChange estimates
RNASeq
DOSE
DESeq2
RNASeq
DOSE
DESeq2
9.6 years ago
Shi, Tao
▴ 720
0
votes
0
replies
1.3k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO
Cancer
Rgraphviz
clusterProfiler
DOSE
GO
Cancer
Rgraphviz
clusterProfiler
DOSE
10.7 years ago
Martin Morgan
25k
0
votes
2
replies
1.3k
views
about limma linear models
Microarray
limma
DOSE
Microarray
limma
DOSE
updated 12.9 years ago by
sense_0109
▴ 40 • written 12.9 years ago by
Gordon Smyth
50k
0
votes
5
replies
1.2k
views
the result of bioconductor not agree with MAS
DOSE
DOSE
updated 21.1 years ago by
"Hüsing, Johannes"
▴ 60 • written 21.1 years ago by
Lang Chen
▴ 100
0
votes
1
reply
1.2k
views
unbalanced design
limma
DOSE
limma
DOSE
updated 19.3 years ago by
Gordon Smyth
50k • written 19.3 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
3
replies
1.2k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE
package installation
windows10
6.7 years ago
Yisong Zhen
▴ 200
0
votes
1
reply
1.2k
views
limma: writing down the matrix in an almost (?) factorial design experiment
Microarray
DOSE
Microarray
DOSE
14.1 years ago
Massimo Pinto
▴ 390
0
votes
0
replies
1.2k
views
robust linear model in anovas
DOSE
DOSE
20.0 years ago
Arne.Muller@aventis.com
▴ 620
0
votes
0
replies
1.2k
views
Expired Illumina expression chip - advice for use and experimental design
GO
limma
DOSE
GO
limma
DOSE
16.2 years ago
Johnstone, Alice
▴ 410
1
vote
1
reply
1.2k
views
dotplot in DOSE
compilation error
DOSE
5.9 years ago
alper.kucukural
▴ 10
0
votes
3
replies
1.2k
views
when do linear models work?
DOSE
DOSE
20.1 years ago
Arne.Muller@aventis.com
▴ 620
0
votes
1
reply
1.1k
views
normalizaton between studies
Normalization
vsn
DOSE
Normalization
vsn
DOSE
updated 19.3 years ago by
Anja.von.Heydebreck@merck.de
▴ 10 • written 19.3 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
0
replies
1.1k
views
microarray analysis of a dose response * strain experiment
Microarray
affy
limma
maSigPro
DOSE
BRAIN
Microarray
affy
limma
maSigPro
DOSE
BRAIN
17.4 years ago
Naomi Altman
★ 6.0k
0
votes
0
replies
1.1k
views
Re: OpenPBS
webbioc
DOSE
webbioc
DOSE
20.4 years ago
Colin A. Smith
▴ 220
0
votes
0
replies
1.1k
views
Re: Classification question(Tom R. Fahland)
Classification
DOSE
Classification
DOSE
19.9 years ago
Stephen Henderson
★ 1.0k
0
votes
0
replies
1.1k
views
about microarray batch effect and treatment effect
affy
DOSE
affy
DOSE
16.3 years ago
Aedin Culhane
▴ 510
0
votes
0
replies
1.1k
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR
DOSE
edgeR
DOSE
10.7 years ago
Sandhya Pemmasani Kiran
▴ 40
50 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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